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Supplemental Methods - ReductomiRs – micro-RNA Signatures in a Reductive Stress Mouse Heart |
Mark E. Pepin MD, PhD |
12 February, 2021 |
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Times |
10pt |
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Justin M. Quiles, Mark E. Pepin, Sini Sunny, Sandeep B. Shelar, Anil K. Challa, Brian Dalley, John R. Hoidal, Steven M. Pogwizd, Adam R. Wende and Namakkal S. Rajasekarana
After alignment of the fastq files to the annotated genome assembly (mm10), the first step in the analysis is to consolidate the raw data from the provided files into data matrix that can be used to generate a normalized count matrix and differential expression dataset.
DESeq2 (version 1.18.1) was used to perform the raw count normalization within R (version 3.4.2)
######### RUN DESeq2
dds<-DESeqDataSetFromMatrix(countData=countData, colData = colData, design= ~Transgene)
dds## class: DESeqDataSet
## dim: 36855 10
## metadata(1): version
## assays(1): counts
## rownames(36855): ENSMUSG00000074183 ENSMUSG00000074181 ...
## ENSMUSG00000064336 ENSMUSG00000064354
## rowData names(0):
## colnames(10): Counts_control0 Counts_control1 ... Counts_TGH1
## Counts_TGH2
## colData names(3): Sample_ID Transgene Treatment
dds$Transgene<-relevel(dds$Transgene, ref = "NO") # setting the reference to wild-type genotype. only relevant for factors.
#Determine the Dispersion Relationship (determines which distribution to use for the differential analysis) - should take about 2 minutes
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
plotDispEsts(dds)
There appears to be a linear negative correlation between the mean and dispersion estimates, so the parametric "Wald" model should be an appropriate fit for differential expression analysis. Furthermore, we could get away with the parametric fit-type, but the run-time is not significantly impaired, allowing us to use the 'local' fit-type. NOTE: If it were nonlinear throughout, we would require a 'local' nonparametric fit-type.
##Pre-Filter to reduce the size of this dataset (according to the DESeq2 document reccomendations)
dds <- dds[ rowSums(counts(dds)) > 1, ]
dds## class: DESeqDataSet
## dim: 21222 10
## metadata(1): version
## assays(2): counts mu
## rownames(21222): ENSMUSG00000074183 ENSMUSG00000074181 ...
## ENSMUSG00000090756 ENSMUSG00000064336
## rowData names(10): baseMean baseVar ... dispOutlier dispMAP
## colnames(10): Counts_control0 Counts_control1 ... Counts_TGH1
## Counts_TGH2
## colData names(4): Sample_ID Transgene Treatment sizeFactor
################Run DESeq2 differential quantification (Likelihood ratio test (LRT), instead of the wald test - easier for large datasets)
dds<-DESeq(dds, test="Wald", fitType="parametric")
#compile the results tables
res<-DESeq2::results(dds)
resdf<-data.frame(res)
resdf$external_gene_name<-row.names(resdf)
resdf$ensembl_gene_id<-resdf$external_gene_nameOnce the differential Expression analysis was performed, the following were compiled into a results data matrix: Log2FoldChange, P-value, Bonferroni-Adjusted P-Value (Q-value), and normalized counts for each sample.
####Add Annotation to the results file (this will take some time, about 5 minutes...)
##Add Gene Information
library(biomaRt)
mmusculus <- biomaRt::useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL",
host = "www.ensembl.org",
dataset = "mmusculus_gene_ensembl",
version = 94)
bm <- getBM(attributes=c("ensembl_gene_id", "external_gene_name", "chromosome_name", "start_position", "end_position"), filter="ensembl_gene_id", values= rownames(dds), mart=mmusculus)
results<-dplyr::left_join(resdf, bm, by = "ensembl_gene_id")
####Add normalized count data (for heatmap and sota)
normcount<-counts(dds)
normcount<-as.data.frame(normcount)
normcount$ensembl_gene_id<-row.names(normcount)
results<-dplyr::left_join(results, normcount, by="ensembl_gene_id")
write.csv(results, "../2_Output/mRNA/results_CaNRF2_mRNA_TG.v.NTG.csv")Before we examined the gene networks and pathways differentially regulated by NRF2 knockout, the first task was to determine whether transgene induction resulted in global changes. An effective way of determining this is the QQ plot, which compares the P-value distribution produced by the pairwise comparison (transgenic vs. WT mouse) to that of a random normal distribution. Below, it is evident that the two experimental groups produce robustly divergent expression patterns consistent with a true population difference worthy of differential expression analysis.
#Create Q-Q plot
test<-results
test<-test[complete.cases(test),]
pQQ(test$pvalue, lim=c(0,10))
In order to visualize the distribution of differentially expressed genes, as well as determine the effect of transgenic intensity (TGH vs. TGL), hierarchical clustering and heatmap visualization were performed at the Q < 0.05 statistical level. This analysis reveals that P < 0.05 is sufficient to separate all samples by genotype. In particular, it is apparent that the TGH group display more robust differential expression than TGL when compared to control, in a sort of dose-dependent manner.
library(pheatmap)
results_p05<-filter(results, padj<0.01)
##Index file for annotating samples
rownames(colData)<-colData$Sample_ID
Index<-dplyr::select(colData, Transgene, Treatment)
Index<-as.data.frame(Index)
rownames(results_p05)<-results_p05$external_gene_name.x
counts_p05<-dplyr::select(results_p05, Counts_control0:Counts_TGH2)
paletteLength <- 100
myColor <- colorRampPalette(c("dodgerblue4", "white", "gold2"))(paletteLength)
pheatmap(counts_p05,
cluster_cols=T,
border_color=NA,
cluster_rows=T,
scale = 'row',
show_colnames = T,
show_rownames = F,
color = myColor,
annotation_col = Index)
Once we established that the populations under consideration truly display divergene expression patterns, we sought to determine whether unbiased global gene expression patterns recapitulate TGL versus TGH phenotypes within the transgenic group. To accomplish this, an unsupervised Principal Components Analysis (PCA) was initially used with normalized counts.
Before running the principal components analysis, it was necessary to first determine the number of PC's required to account for 80% of the variance, a machine-learning algorithmm benchmark that provides sufficient confidence in the analysis.
#Plot Features of the PCA
library(readxl)
library(dplyr)
library(plotly)
##Import the data to be used for PCA
results_DEG<-dplyr::select(results, Counts_control0:Counts_TGH2)
results_DEG<-results_DEG[order(-rowSums(results_DEG)),]
#transpose the dataset (required for PCA)
data.pca<-t(results_DEG)
data.pca<-as.data.frame(data.pca)
##Import the data to be used for annotation
rownames(colData)<-colData$Sample_ID
Index<-dplyr::select(colData, Transgene, Treatment)
Index<-as.data.frame(Index)
##merge the file
data.pca_Final<-merge(Index, data.pca, by=0)
rownames(data.pca_Final)<-data.pca_Final$Row.names
pca.comp<-prcomp(data.pca_Final[,(ncol(Index)+2):ncol(data.pca_Final)])
pcaCharts=function(x) {
x.var <- x$sdev ^ 2
x.pvar <- x.var/sum(x.var)
par(mfrow=c(2,2))
plot(x.pvar,xlab="Principal component",
ylab="Proportion of variance", ylim=c(0,1), type='b')
plot(cumsum(x.pvar),xlab="Principal component",
ylab="Cumulative Proportion of variance",
ylim=c(0,1),
type='b')
screeplot(x)
screeplot(x,type="l")
par(mfrow=c(1,1))
}
pcaCharts(pca.comp)
From the previous calculations, it is seens that only 2 principal components are necessary (accounting for >80% cumulative variance). Nonetheless, below is a 3-D PCA to ensure that all groups are characterize to higher-degree of stringency.
##Create a 3D-PCA for Inspection
PCs<-merge(pca.comp$x, Index, by=0)
rownames(PCs)<-PCs$Row.names
ax_text<-list(
family = "times",
size = 12,
color = "black")
t <- list(
family = "times",
size = 14,
color = "black")
p <- plot_ly(PCs, x = ~PC1, y = ~PC2, z = ~PC3,
marker = list(color = ~Treatment,
colorscale = c('#FFE1A1', '#683531'),
showscale = FALSE)) %>%
add_markers() %>%
layout(scene = list(
xaxis = list(title = 'PC1', zerolinewidth = 4,
zerolinecolor="darkgrey", linecolor="darkgrey",
linewidth=4, titlefont=t, tickfont=ax_text),
yaxis = list(title = 'PC2', zerolinewidth = 4,
zerolinecolor="darkgrey", linecolor="darkgrey",
linewidth=4, titlefont=t, tickfont=ax_text),
zaxis = list(title = 'PC3', zerolinewidth = 4,
zerolinecolor="darkgrey", linecolor="darkgrey",
linewidth=4, titlefont=t, tickfont=ax_text)),
annotations = list(
x = 1.13,
y = 1.03,
text = 'Transgene',
xref = '1',
yref = '0',
showarrow = FALSE))
p #must comment out for PDF generation via knitr (Pandoc)<div id="htmlwidget-31e876b1dcf983ad8560" style="width:672px;height:480px;" class="plotly html-widget"></div>
<script type="application/json" data-for="htmlwidget-31e876b1dcf983ad8560">{"x":{"visdat":{"24163516c15f":["function () ","plotlyVisDat"]},"cur_data":"24163516c15f","attrs":{"24163516c15f":{"x":{},"y":{},"z":{},"marker":{"color":{},"colorscale":["#FFE1A1","#683531"],"showscale":false},"alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"scatter3d","mode":"markers","inherit":true}},"layout":{"margin":{"b":40,"l":60,"t":25,"r":10},"scene":{"xaxis":{"title":"PC1","zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":14,"color":"black"},"tickfont":{"family":"times","size":12,"color":"black"}},"yaxis":{"title":"PC2","zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":14,"color":"black"},"tickfont":{"family":"times","size":12,"color":"black"}},"zaxis":{"title":"PC3","zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":14,"color":"black"},"tickfont":{"family":"times","size":12,"color":"black"}}},"annotations":[{"x":1.13,"y":1.03,"text":"Transgene","xref":"1","yref":"0","showarrow":false}],"hovermode":"closest","showlegend":false},"source":"A","config":{"showSendToCloud":false},"data":[{"x":[-80685.8062266134,-179159.155038288,-71174.6020569514,-98837.6818655239,107209.915862281,67172.1023848943,126782.66993385,64335.4461343561,57861.2685138884,6495.84235810865],"y":[23486.2585286078,-39290.1380681,29022.5261011266,-26215.9471145263,-6260.94379780434,-117205.227779094,-31131.4968746382,43324.0712417056,62823.1246480386,61447.7731146841],"z":[62003.199332036,8027.62969924111,-102319.112373534,19828.7311181967,4883.69474409674,-25376.6388502875,26310.5409484113,7892.67591266029,-29904.3191763238,28653.5986455029],"marker":{"color":[0,0,0,0,2,2,2,1,1,1],"colorscale":["#FFE1A1","#683531"],"showscale":false,"line":{"color":"rgba(31,119,180,1)"}},"type":"scatter3d","mode":"markers","error_y":{"color":"rgba(31,119,180,1)"},"error_x":{"color":"rgba(31,119,180,1)"},"line":{"color":"rgba(31,119,180,1)"},"frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.2,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script>
library(ggfortify)
library(cluster)
autoplot(pca.comp, data = data.pca_Final, colour = "Treatment")
# Format for Correlation
library(corrplot)
library(Hmisc)
cor<-data.matrix((counts_p05))
cor.m<-rcorr(cor)
cor.r<-cor(cor)
paletteLength <- 100
myColor <- colorRampPalette(c("dodgerblue4", "white", "brown4"))(paletteLength)
p.mat<-cor.mtest(cor.r)$p
paletteLength <- 100
myColor <- colorRampPalette(c("black", "white","firebrick"))(paletteLength)
pheatmap(cor.r,
clustering_method = "single",
cutree_rows = 3,
cutree_cols = 3,
cluster_cols=T,
border_color=NA,
cluster_rows=T,
scale = "none",
show_colnames = F,
show_rownames = F,
color = myColor,
annotation_col = Index)
To determine the effect of miRNA, as well as identify the putative miRNA disregulated in a dose-dependent manner, miRNA-sequencing was performed on the same samples as before.
DESeq2 (version 1.18.1) was used to perform the raw count normalization within R (version 3.4.2)
######### RUN DESeq2
dds_mir<-DESeqDataSetFromMatrix(countData=countData_mir, colData = colData_mir, design= ~Transgene)
dds_mir## class: DESeqDataSet
## dim: 623 9
## metadata(1): version
## assays(1): counts
## rownames(623): mmu-miR-1929-5p mmu-miR-1930-5p ... mmu-miR-215-3p
## mmu-miR-7236-3p
## rowData names(0):
## colnames(9): Counts_control0 Counts_control1 ... Counts_TGH1
## Counts_TGH2
## colData names(3): Sample_ID Transgene Treatment
dds_mir$Transgene<-relevel(dds_mir$Transgene, ref = "NO") # setting the reference to wild-type genotype. only relevant for factors.
#Determine the Dispersion Relationship (determines which distribution to use for the differential analysis) - should take about 2 minutes
dds_mir <- estimateSizeFactors(dds_mir)
dds_mir <- estimateDispersions(dds_mir)
plotDispEsts(dds_mir)
There appears to be a linear negative correlation between the mean and dispersion estimates, so the parametric "Wald" model should be an appropriate fit for differential expression analysis. Furthermore, we could get away with the parametric fit-type, but the run-time is not significantly impaired, allowing us to use the 'local' fit-type. NOTE: If it were nonlinear throughout, we would require a 'local' nonparametric fit-type.
##Pre-Filter to reduce the size of this dataset (according to the DESeq2 document reccomendations)
dds_mir <- dds_mir[ rowSums(counts(dds_mir)) > 1, ]
dds_mir## class: DESeqDataSet
## dim: 623 9
## metadata(1): version
## assays(2): counts mu
## rownames(623): mmu-miR-1929-5p mmu-miR-1930-5p ... mmu-miR-215-3p
## mmu-miR-7236-3p
## rowData names(10): baseMean baseVar ... dispOutlier dispMAP
## colnames(9): Counts_control0 Counts_control1 ... Counts_TGH1
## Counts_TGH2
## colData names(4): Sample_ID Transgene Treatment sizeFactor
################Run DESeq2 differential quantification (Likelihood ratio test (LRT), instead of the wald test - easier for large datasets)
dds_mir<-DESeq(dds_mir, test="Wald", fitType="parametric")
#compile the results tables
res_mir<-DESeq2::results(dds_mir)
resdf_mir<-data.frame(res_mir)
resdf_mir$external_gene_name<-row.names(resdf_mir)
resdf_mir$ensembl_gene_id<-resdf_mir$external_gene_nameOnce the differential Expression analysis was performed, the following were compiled into a results data matrix: Log2FoldChange, P-value, Bonferroni-Adjusted P-Value (Q-value), and normalized counts for each sample.
####Add normalized count data (for heatmap and sota)
normcount_mir<-counts(dds_mir)
normcount_mir<-as.data.frame(normcount_mir)
normcount_mir$ensembl_gene_id<-row.names(normcount_mir)
results_mir<-dplyr::left_join(resdf_mir, normcount_mir, by="ensembl_gene_id")
rownames(results_mir)<-results_mir$external_gene_nameBefore we examined the gene networks and pathways differentially regulated by NRF2 knockout, the first task was to determine whether transgene induction resulted in global changes. An effective way of determining this is the QQ plot, which compares the P-value distribution produced by the pairwise comparison (transgenic vs. WT mouse) to that of a random normal distribution. Below, it is evident that the two experimental groups produce robustly divergent expression patterns consistent with a true population difference worthy of differential expression analysis.
#Create Q-Q plot
results_mir<-results_mir[complete.cases(results_mir),]
write.csv(results_mir, "../2_Output/miRNA/results_miRNA_TG.v.NTG.csv")
pQQ(results_mir$pvalue, lim=c(0,10))
In order to visualize the distribution of differentially expressed genes, as well as determine the effect of transgenic intensity (TGH vs. TGL), hierarchical clustering and heatmap visualization were performed at the Q < 0.05 statistical level. This analysis reveals that P < 0.05 is sufficient to separate all samples by genotype. In particular, it is apparent that the TGH group display more robust differential expression than TGL when compared to control, in a sort of dose-dependent manner.
library(pheatmap)
results_p05_mir<-filter(results_mir, padj<.01)
rownames(results_p05_mir)<-results_p05_mir$ensembl_gene_id
##Index file for annotating samples
rownames(colData_mir)<-colData_mir$Sample_ID
Index_mir<-dplyr::select(colData_mir, Transgene, Treatment)
Index_mir<-as.data.frame(Index_mir)
counts_p05_mir<-dplyr::select(results_p05_mir, Counts_control0:Counts_TGH2)
paletteLength <- 100
myColor <- colorRampPalette(c("dodgerblue4", "white", "gold2"))(paletteLength)
pheatmap(counts_p05_mir,
cluster_cols=T,
border_color=NA,
cluster_rows=T,
scale = 'row',
show_colnames = T,
show_rownames = T,
color = myColor,
annotation_col = Index_mir)
Once we established that the populations under consideration truly display divergene expression patterns, we sought to determine whether unbiased global gene expression patterns recapitulate TGL versus TGH phenotypes within the transgenic group. To accomplish this, an unsupervised Principal Components Analysis (PCA) was initially used with normalized counts.
Before running the principal components analysis, it was necessary to first determine the number of PC's required to account for 80% of the variance, a machine-learning algorithmm benchmark that provides sufficient confidence in the analysis.
#Plot Features of the PCA
library(readxl)
library(dplyr)
library(plotly)
##Import the data to be used for PCA
results_dmir<-dplyr::select(results_mir, Counts_control0:Counts_TGH2)
results_dmir<-results_dmir[order(-rowSums(results_dmir)),]
#transpose the dataset (required for PCA)
data.pca_dmir<-t(results_dmir)
data.pca_dmir<-as.data.frame(data.pca_dmir)
##Import the data to be used for annotation
rownames(colData_mir)<-colData_mir$Sample_ID
Index_mir<-dplyr::select(colData_mir, Transgene, Treatment)
Index_mir<-as.data.frame(Index_mir)
##merge the file
data.pca_Final_dmir<-merge(Index_mir, data.pca_dmir, by=0)
rownames(data.pca_Final_dmir)<-data.pca_Final_dmir$Row.names
pca.comp_dmir<-prcomp(data.pca_Final_dmir[,(ncol(Index_mir)+2):ncol(data.pca_Final_dmir)])
pcaCharts=function(x) {
x.var <- x$sdev ^ 2
x.pvar <- x.var/sum(x.var)
par(mfrow=c(2,2))
plot(x.pvar,xlab="Principal component",
ylab="Proportion of variance", ylim=c(0,1), type='b')
plot(cumsum(x.pvar),xlab="Principal component",
ylab="Cumulative Proportion of variance",
ylim=c(0,1),
type='b')
screeplot(x)
screeplot(x,type="l")
par(mfrow=c(1,1))
}
pcaCharts(pca.comp_dmir)
From the previous calculations, it is seens that again only 2 principal components are necessary (accounting for >80% cumulative variance). Nonetheless, below is a 3-D PCA to ensure that all groups are characterize to higher-degree of stringency.
##Create a 3D-PCA for Inspection
PCs_mir<-merge(pca.comp_dmir$x, Index_mir, by=0)
rownames(PCs_mir)<-PCs_mir$Row.names
ax_text<-list(
family = "times",
size = 12,
color = "black")
t <- list(
family = "times",
size = 14,
color = "black")
p_mir <- plot_ly(PCs_mir, x = ~PC1, y = ~PC2, z = ~PC3,
marker = list(color = ~Treatment,
colorscale = c('#FFE1A1', '#683531'),
showscale = TRUE)) %>%
add_markers() %>%
layout(scene = list(
xaxis = list(title = 'PC1', zerolinewidth = 4,
zerolinecolor="darkgrey", linecolor="darkgrey",
linewidth=4, titlefont=t, tickfont=ax_text),
yaxis = list(title = 'PC2', zerolinewidth = 4,
zerolinecolor="darkgrey", linecolor="darkgrey",
linewidth=4, titlefont=t, tickfont=ax_text),
zaxis = list(title = 'PC3', zerolinewidth = 4,
zerolinecolor="darkgrey", linecolor="darkgrey",
linewidth=4, titlefont=t, tickfont=ax_text)),
annotations = list(
x = 1.13,
y = 1.03,
text = 'Transgene',
xref = '1',
yref = '0',
showarrow = FALSE))
p_mir #must comment out for PDF generation via knitr (Pandoc)<div id="htmlwidget-06f03b8417e95a29f241" style="width:672px;height:480px;" class="plotly html-widget"></div>
<script type="application/json" data-for="htmlwidget-06f03b8417e95a29f241">{"x":{"visdat":{"241669d94da1":["function () ","plotlyVisDat"]},"cur_data":"241669d94da1","attrs":{"241669d94da1":{"x":{},"y":{},"z":{},"marker":{"color":{},"colorscale":["#FFE1A1","#683531"],"showscale":true},"alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"scatter3d","mode":"markers","inherit":true}},"layout":{"margin":{"b":40,"l":60,"t":25,"r":10},"scene":{"xaxis":{"title":"PC1","zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":14,"color":"black"},"tickfont":{"family":"times","size":12,"color":"black"}},"yaxis":{"title":"PC2","zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":14,"color":"black"},"tickfont":{"family":"times","size":12,"color":"black"}},"zaxis":{"title":"PC3","zerolinewidth":4,"zerolinecolor":"darkgrey","linecolor":"darkgrey","linewidth":4,"titlefont":{"family":"times","size":14,"color":"black"},"tickfont":{"family":"times","size":12,"color":"black"}}},"annotations":[{"x":1.13,"y":1.03,"text":"Transgene","xref":"1","yref":"0","showarrow":false}],"hovermode":"closest","showlegend":false},"source":"A","config":{"showSendToCloud":false},"data":[{"x":[-364099.114849777,-27848.3270209532,685304.043075243,-306626.804485747,1042668.88413052,-1238285.56331604,135199.751481609,-111266.785230066,184953.91621521],"y":[-131098.197382159,-181984.00866072,-260451.615673919,140847.573845181,216038.02073061,9313.19811924191,104311.332558053,263336.513228046,-160312.816764333],"z":[220571.897722433,-71422.2706723823,56713.1727055869,-157348.735859851,-142619.069426904,-127041.807137686,190804.648758678,164776.726556951,-134434.562646827],"marker":{"color":[0,0,0,2,2,2,1,1,1],"colorscale":["#FFE1A1","#683531"],"showscale":true,"line":{"color":"rgba(31,119,180,1)"}},"type":"scatter3d","mode":"markers","error_y":{"color":"rgba(31,119,180,1)"},"error_x":{"color":"rgba(31,119,180,1)"},"line":{"color":"rgba(31,119,180,1)"},"frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.2,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script>
library(ggfortify)
library(cluster)
autoplot(pca.comp_dmir, data = data.pca_Final_dmir, colour = "Treatment")
In order to identify the response elements likely targeted by Nfe2l2 (Nrf2) we used the position-weighted matrix (PWM) generated by Brochley et al. We scanned the mus musculus genome (mm10) for all Nrf2 (Nfe2l2) response elements using the Nfe2l2 PWM via PWMScan (Ambrosini 2018); this process identified 80,756 Nrf2 response elements throughout the mouse genome. These genomic coordinates were then used to determine which differentially-expressed miRNA are likely under the control of Nrf2 based on the presents of Antioxidant Response Elements upstream of the miRNA coding region.
AC MA0150.2
XX
ID Nfe2l2
XX
DE MA0150.2 Nfe2l2 ; From JASPAR 2018
PO A C G T
01 278 23 103 6
02 0 2 0 408
03 0 0 400 10
04 410 0 0 0
05 14 287 74 35
06 52 11 11 336
07 26 315 30 39
08 329 2 47 32
09 3 3 404 0
10 3 398 6 3
11 346 13 15 36
XX
// \
Once the Nfe2l2 response elements were identified, we used Hypergeometric Optimization for Motif Enrichment (HOMER) to annotate these genomic regions according to the most proximal gene. The following command was used: annotatePeaks pwmscan_mm10_40220_40766.bed mm10 > Nfe2l2_REs.Genome.txt.
| PeakID..cmd.annotatePeaks.pl.pwmscan_mm10_40220_40766.bed.mm10. | Chr | Start | End | Strand | Peak.Score | Focus.Ratio.Region.Size | Annotation | Detailed.Annotation | Distance.to.TSS | Nearest.PromoterID | Entrez.ID | Nearest.Unigene | Nearest.Refseq | Nearest.Ensembl | Gene.Name | Gene.Alias | Gene.Description | Gene.Type |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ATGACTCAGCA-1912 | chr6 | 82702040 | 82702050 | + | 1959 | Intergenic | B2_Mm2|SINE|B2 | -49180 | NM_025882 | 66979 | Mm.195753 | NM_025882 | ENSMUSG00000030042 | Pole4 | 2400007P05Rik|5830430F06Rik | polymerase (DNA-directed), epsilon 4 (p12 subunit) | protein-coding | |
| ATGACTCAGCA-4868 | chr17 | 64662442 | 64662452 | - | 1959 | intron (NM_008549, intron 6 of 21) | B2_Mm2|SINE|B2 | 60798 | NM_008549 | 17158 | Mm.2433 | NM_008549 | ENSMUSG00000024085 | Man2a1 | Mana-2|Mana2|Map-2 | mannosidase 2, alpha 1 | protein-coding | |
| ATGACTCAGCA-1928 | chr6 | 87853595 | 87853605 | + | 1959 | Intergenic | Intergenic | -2494 | NM_001355195 | 12785 | Mm.290251 | NM_013493 | ENSMUSG00000030057 | Cnbp | AA408710|Cnbp1|Znf9 | cellular nucleic acid binding protein | protein-coding | |
| ATGACTCAGCA-405 | chr1 | 191471513 | 191471523 | - | 1959 | Intergenic | RSINE1|SINE|B4 | -6470 | NR_151615 | 102634668 | NR_151615 | Gm32200 | - | predicted gene, 32200 | ncRNA | |||
| ATGACTCAGCA-1617 | chr5 | 100753629 | 100753639 | + | 1959 | Intergenic | MamSINE1|SINE|tRNA | -33918 | NM_152803 | 15442 | Mm.265786 | NM_152803 | ENSMUSG00000035273 | Hpse | HSE1|Hpa|Hpr1 | heparanase | protein-coding | |
| ATGACTCAGCA-4388 | chr15 | 36657700 | 36657710 | - | 1959 | Intergenic | Intergenic | -48732 | NM_008774 | 18458 | Mm.371570 | NM_008774 | ENSMUSG00000022283 | Pabpc1 | PABP|Pabp1|PabpI|Pabpl1|ePAB | poly(A) binding protein, cytoplasmic 1 | protein-coding |
We then inspected the list of miRNA that were only differentially-expressed in the Dose Effect (TgH vs. TgL, excluding Tg vs. NTg). From this, we found that 20 of the 40 differentially-expressed miRNA contained at least 1 Nrf2 response element in the most-proximal promoter region.
## Searching diana_microt ...
## Searching elmmo ...
## Searching microcosm ...
## Searching miranda ...
## Searching mirdb ...
## Searching pictar ...
## Searching pita ...
## Searching targetscan ...
The next component of this analysis was to determine whether upstream miRNA have overlapping predicted downstream mRNA targets. To accomplish this aim, a bipartite network analysis was created to depict (1) the differentially-expressed miRNA containing a proximal upstream Nrf2 response element, and (2) their downstream predicted mRNA targets identified via multiMiR.
All packages and setting are acquired using the following command:
## setting value
## version R version 4.0.3 (2020-10-10)
## os macOS Big Sur 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Berlin
## date 2021-02-12
| package | ondiskversion | loadedversion | path | loadedpath | attached | is_base | date | source | md5ok | library | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| annotate | annotate | 1.68.0 | 1.68.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/annotate | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/annotate | FALSE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| AnnotationDbi | AnnotationDbi | 1.52.0 | 1.52.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/AnnotationDbi | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/AnnotationDbi | FALSE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| askpass | askpass | 1.1 | 1.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/askpass | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/askpass | FALSE | FALSE | 2019-01-13 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| assertthat | assertthat | 0.2.1 | 0.2.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/assertthat | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/assertthat | FALSE | FALSE | 2019-03-21 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| backports | backports | 1.2.1 | 1.2.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/backports | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/backports | FALSE | FALSE | 2020-12-09 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| base64enc | base64enc | 0.1.3 | 0.1-3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/base64enc | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/base64enc | FALSE | FALSE | 2015-07-28 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| Biobase | Biobase | 2.50.0 | 2.50.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biobase | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biobase | TRUE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| BiocFileCache | BiocFileCache | 1.14.0 | 1.14.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocFileCache | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocFileCache | FALSE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| BiocGenerics | BiocGenerics | 0.36.0 | 0.36.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocGenerics | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocGenerics | TRUE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| BiocManager | BiocManager | 1.30.10 | 1.30.10 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocManager | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocManager | TRUE | FALSE | 2019-11-16 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| BiocParallel | BiocParallel | 1.24.1 | 1.24.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocParallel | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BiocParallel | FALSE | FALSE | 2020-11-06 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| biomaRt | biomaRt | 2.46.3 | 2.46.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/biomaRt | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/biomaRt | TRUE | FALSE | 2021-02-09 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| bipartite | bipartite | 2.16 | 2.16 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bipartite | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bipartite | TRUE | FALSE | 2021-02-04 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| bit | bit | 4.0.4 | 4.0.4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bit | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bit | FALSE | FALSE | 2020-08-04 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| bit64 | bit64 | 4.0.5 | 4.0.5 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bit64 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bit64 | FALSE | FALSE | 2020-08-30 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| bitops | bitops | 1.0.6 | 1.0-6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bitops | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bitops | FALSE | FALSE | 2013-08-17 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| blob | blob | 1.2.1 | 1.2.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/blob | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/blob | FALSE | FALSE | 2020-01-20 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| cachem | cachem | 1.0.3 | 1.0.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cachem | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cachem | FALSE | FALSE | 2021-02-04 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| calibrate | calibrate | 1.7.7 | 1.7.7 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/calibrate | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/calibrate | TRUE | FALSE | 2020-06-19 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| callr | callr | 3.5.1 | 3.5.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/callr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/callr | FALSE | FALSE | 2020-10-13 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| cellranger | cellranger | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cellranger | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cellranger | FALSE | FALSE | 2016-07-27 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| checkmate | checkmate | 2.0.0 | 2.0.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/checkmate | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/checkmate | FALSE | FALSE | 2020-02-06 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| cli | cli | 2.3.0 | 2.3.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cli | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cli | FALSE | FALSE | 2021-01-31 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| cluster | cluster | 2.1.0 | 2.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cluster | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cluster | TRUE | FALSE | 2019-06-19 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| coda | coda | 0.19.4 | 0.19-4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/coda | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/coda | FALSE | FALSE | 2020-09-30 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| codetools | codetools | 0.2.18 | 0.2-18 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/codetools | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/codetools | FALSE | FALSE | 2020-11-04 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| colorspace | colorspace | 2.0.0 | 2.0-0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/colorspace | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/colorspace | FALSE | FALSE | 2020-11-11 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| corrplot | corrplot | 0.84 | 0.84 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/corrplot | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/corrplot | TRUE | FALSE | 2017-10-16 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| crayon | crayon | 1.4.1 | 1.4.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/crayon | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/crayon | FALSE | FALSE | 2021-02-08 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| crosstalk | crosstalk | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/crosstalk | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/crosstalk | FALSE | FALSE | 2021-01-12 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| curl | curl | 4.3 | 4.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/curl | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/curl | FALSE | FALSE | 2019-12-02 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| data.table | data.table | 1.13.6 | 1.13.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.table | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.table | TRUE | FALSE | 2020-12-30 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| DBI | DBI | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/DBI | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/DBI | FALSE | FALSE | 2021-01-15 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| dbplyr | dbplyr | 2.1.0 | 2.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/dbplyr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/dbplyr | FALSE | FALSE | 2021-02-03 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| DelayedArray | DelayedArray | 0.16.1 | 0.16.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/DelayedArray | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/DelayedArray | FALSE | FALSE | 2021-01-22 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| desc | desc | 1.2.0 | 1.2.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/desc | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/desc | FALSE | FALSE | 2018-05-01 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| DESeq2 | DESeq2 | 1.30.0 | 1.30.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/DESeq2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/DESeq2 | TRUE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| devtools | devtools | 2.3.2 | 2.3.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/devtools | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/devtools | FALSE | FALSE | 2020-09-18 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| digest | digest | 0.6.27 | 0.6.27 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/digest | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/digest | FALSE | FALSE | 2020-10-24 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| dotCall64 | dotCall64 | 1.0.0 | 1.0-0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/dotCall64 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/dotCall64 | FALSE | FALSE | 2018-07-30 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| dplyr | dplyr | 1.0.4 | 1.0.4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/dplyr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/dplyr | TRUE | FALSE | 2021-02-02 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| ellipsis | ellipsis | 0.3.1 | 0.3.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ellipsis | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ellipsis | FALSE | FALSE | 2020-05-15 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| evaluate | evaluate | 0.14 | 0.14 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/evaluate | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/evaluate | FALSE | FALSE | 2019-05-28 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| farver | farver | 2.0.3 | 2.0.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/farver | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/farver | FALSE | FALSE | 2020-01-16 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| fastmap | fastmap | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/fastmap | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/fastmap | FALSE | FALSE | 2021-01-25 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| ff | ff | 4.0.4 | 4.0.4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ff | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ff | FALSE | FALSE | 2020-10-13 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| fields | fields | 11.6 | 11.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/fields | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/fields | FALSE | FALSE | 2020-10-09 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| foreign | foreign | 0.8.81 | 0.8-81 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/foreign | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/foreign | FALSE | FALSE | 2020-12-22 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| Formula | Formula | 1.2.4 | 1.2-4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Formula | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Formula | TRUE | FALSE | 2020-10-16 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| fs | fs | 1.5.0 | 1.5.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/fs | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/fs | FALSE | FALSE | 2020-07-31 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| genefilter | genefilter | 1.72.1 | 1.72.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/genefilter | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/genefilter | FALSE | FALSE | 2021-01-21 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| geneplotter | geneplotter | 1.68.0 | 1.68.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/geneplotter | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/geneplotter | FALSE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| generics | generics | 0.1.0 | 0.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/generics | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/generics | FALSE | FALSE | 2020-10-31 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| GenomeInfoDb | GenomeInfoDb | 1.26.2 | 1.26.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/GenomeInfoDb | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/GenomeInfoDb | TRUE | FALSE | 2020-12-08 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| GenomeInfoDbData | GenomeInfoDbData | 1.2.4 | 1.2.4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/GenomeInfoDbData | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/GenomeInfoDbData | FALSE | FALSE | 2020-11-16 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| GenomicRanges | GenomicRanges | 1.42.0 | 1.42.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/GenomicRanges | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/GenomicRanges | TRUE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| ggfortify | ggfortify | 0.4.11 | 0.4.11 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ggfortify | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ggfortify | TRUE | FALSE | 2020-10-02 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| ggplot2 | ggplot2 | 3.3.3 | 3.3.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ggplot2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ggplot2 | TRUE | FALSE | 2020-12-30 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| glue | glue | 1.4.2 | 1.4.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/glue | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/glue | FALSE | FALSE | 2020-08-27 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| gridExtra | gridExtra | 2.3 | 2.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/gridExtra | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/gridExtra | FALSE | FALSE | 2017-09-09 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| gtable | gtable | 0.3.0 | 0.3.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/gtable | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/gtable | FALSE | FALSE | 2019-03-25 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| Haplin | Haplin | 7.2.3 | 7.2.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Haplin | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Haplin | TRUE | FALSE | 2020-09-07 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| highr | highr | 0.8 | 0.8 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/highr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/highr | FALSE | FALSE | 2019-03-20 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| Hmisc | Hmisc | 4.4.2 | 4.4-2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Hmisc | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Hmisc | TRUE | FALSE | 2020-11-29 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| hms | hms | 1.0.0 | 1.0.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/hms | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/hms | FALSE | FALSE | 2021-01-13 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| htmlTable | htmlTable | 2.1.0 | 2.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/htmlTable | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/htmlTable | FALSE | FALSE | 2020-09-16 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| htmltools | htmltools | 0.5.1.1 | 0.5.1.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/htmltools | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/htmltools | FALSE | FALSE | 2021-01-22 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| htmlwidgets | htmlwidgets | 1.5.3 | 1.5.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/htmlwidgets | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/htmlwidgets | FALSE | FALSE | 2020-12-10 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| httr | httr | 1.4.2 | 1.4.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/httr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/httr | FALSE | FALSE | 2020-07-20 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| igraph | igraph | 1.2.6 | 1.2.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/igraph | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/igraph | FALSE | FALSE | 2020-10-06 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| IRanges | IRanges | 2.24.1 | 2.24.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges | TRUE | FALSE | 2020-12-12 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| jpeg | jpeg | 0.1.8.1 | 0.1-8.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/jpeg | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/jpeg | FALSE | FALSE | 2019-10-24 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| jsonlite | jsonlite | 1.7.2 | 1.7.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/jsonlite | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/jsonlite | FALSE | FALSE | 2020-12-09 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| kableExtra | kableExtra | 1.3.1 | 1.3.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/kableExtra | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/kableExtra | TRUE | FALSE | 2020-10-22 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| knitr | knitr | 1.31 | 1.31 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/knitr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/knitr | TRUE | FALSE | 2021-01-27 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| labeling | labeling | 0.4.2 | 0.4.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/labeling | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/labeling | FALSE | FALSE | 2020-10-20 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| lattice | lattice | 0.20.41 | 0.20-41 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/lattice | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/lattice | TRUE | FALSE | 2020-04-02 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| latticeExtra | latticeExtra | 0.6.29 | 0.6-29 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/latticeExtra | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/latticeExtra | FALSE | FALSE | 2019-12-19 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| lazyeval | lazyeval | 0.2.2 | 0.2.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/lazyeval | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/lazyeval | FALSE | FALSE | 2019-03-15 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| lifecycle | lifecycle | 0.2.0 | 0.2.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/lifecycle | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/lifecycle | FALSE | FALSE | 2020-03-06 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| locfit | locfit | 1.5.9.4 | 1.5-9.4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/locfit | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/locfit | FALSE | FALSE | 2020-03-25 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| magrittr | magrittr | 2.0.1 | 2.0.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/magrittr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/magrittr | FALSE | FALSE | 2020-11-17 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| maps | maps | 3.3.0 | 3.3.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/maps | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/maps | FALSE | FALSE | 2018-04-03 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| MASS | MASS | 7.3.53 | 7.3-53 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MASS | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MASS | TRUE | FALSE | 2020-09-09 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| Matrix | Matrix | 1.3.2 | 1.3-2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix | FALSE | FALSE | 2021-01-06 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| MatrixGenerics | MatrixGenerics | 1.2.1 | 1.2.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MatrixGenerics | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/MatrixGenerics | TRUE | FALSE | 2021-01-30 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| matrixStats | matrixStats | 0.58.0 | 0.58.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/matrixStats | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/matrixStats | TRUE | FALSE | 2021-01-29 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| memoise | memoise | 2.0.0 | 2.0.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/memoise | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/memoise | FALSE | FALSE | 2021-01-26 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| mgcv | mgcv | 1.8.33 | 1.8-33 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/mgcv | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/mgcv | FALSE | FALSE | 2020-08-27 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| multiMiR | multiMiR | 1.12.0 | 1.12.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/multiMiR | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/multiMiR | TRUE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| munsell | munsell | 0.5.0 | 0.5.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/munsell | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/munsell | FALSE | FALSE | 2018-06-12 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| network | network | 1.16.1 | 1.16.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/network | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/network | TRUE | FALSE | 2020-10-07 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| nlme | nlme | 3.1.152 | 3.1-152 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/nlme | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/nlme | FALSE | FALSE | 2021-02-04 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| nnet | nnet | 7.3.15 | 7.3-15 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/nnet | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/nnet | FALSE | FALSE | 2021-01-24 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| openssl | openssl | 1.4.3 | 1.4.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/openssl | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/openssl | FALSE | FALSE | 2020-09-18 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| permute | permute | 0.9.5 | 0.9-5 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/permute | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/permute | TRUE | FALSE | 2019-03-12 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| pheatmap | pheatmap | 1.0.12 | 1.0.12 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pheatmap | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pheatmap | TRUE | FALSE | 2019-01-04 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| pillar | pillar | 1.4.7 | 1.4.7 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pillar | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pillar | FALSE | FALSE | 2020-11-20 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| pkgbuild | pkgbuild | 1.2.0 | 1.2.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pkgbuild | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pkgbuild | FALSE | FALSE | 2020-12-15 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| pkgconfig | pkgconfig | 2.0.3 | 2.0.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pkgconfig | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pkgconfig | FALSE | FALSE | 2019-09-22 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| pkgload | pkgload | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pkgload | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/pkgload | FALSE | FALSE | 2020-05-29 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| plotly | plotly | 4.9.3 | 4.9.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/plotly | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/plotly | TRUE | FALSE | 2021-01-10 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| png | png | 0.1.7 | 0.1-7 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/png | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/png | FALSE | FALSE | 2013-12-03 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| prettyunits | prettyunits | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/prettyunits | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/prettyunits | FALSE | FALSE | 2020-01-24 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| processx | processx | 3.4.5 | 3.4.5 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/processx | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/processx | FALSE | FALSE | 2020-11-30 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| progress | progress | 1.2.2 | 1.2.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/progress | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/progress | FALSE | FALSE | 2019-05-16 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| ps | ps | 1.5.0 | 1.5.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ps | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/ps | FALSE | FALSE | 2020-12-05 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| purrr | purrr | 0.3.4 | 0.3.4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/purrr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/purrr | FALSE | FALSE | 2020-04-17 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| R6 | R6 | 2.5.0 | 2.5.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/R6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/R6 | FALSE | FALSE | 2020-10-28 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rappdirs | rappdirs | 0.3.3 | 0.3.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rappdirs | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rappdirs | FALSE | FALSE | 2021-01-31 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| RColorBrewer | RColorBrewer | 1.1.2 | 1.1-2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RColorBrewer | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RColorBrewer | TRUE | FALSE | 2014-12-07 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| Rcpp | Rcpp | 1.0.6 | 1.0.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp | FALSE | FALSE | 2021-01-15 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| RCurl | RCurl | 1.98.1.2 | 1.98-1.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RCurl | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RCurl | FALSE | FALSE | 2020-04-18 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| readxl | readxl | 1.3.1 | 1.3.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/readxl | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/readxl | TRUE | FALSE | 2019-03-13 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| remotes | remotes | 2.2.0 | 2.2.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/remotes | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/remotes | FALSE | FALSE | 2020-07-21 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rlang | rlang | 0.4.10 | 0.4.10 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rlang | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rlang | FALSE | FALSE | 2020-12-30 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rle | rle | 0.9.2 | 0.9.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rle | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rle | FALSE | FALSE | 2020-09-25 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rmarkdown | rmarkdown | 2.6 | 2.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown | FALSE | FALSE | 2020-12-14 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rpart | rpart | 4.1.15 | 4.1-15 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rpart | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rpart | FALSE | FALSE | 2019-04-12 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rprojroot | rprojroot | 2.0.2 | 2.0.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rprojroot | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rprojroot | FALSE | FALSE | 2020-11-15 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| RSQLite | RSQLite | 2.2.3 | 2.2.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSQLite | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSQLite | FALSE | FALSE | 2021-01-24 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rstudioapi | rstudioapi | 0.13 | 0.13 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstudioapi | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstudioapi | FALSE | FALSE | 2020-11-12 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| rvest | rvest | 0.3.6 | 0.3.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rvest | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rvest | FALSE | FALSE | 2020-07-25 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| S4Vectors | S4Vectors | 0.28.1 | 0.28.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors | TRUE | FALSE | 2020-12-09 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| scales | scales | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/scales | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/scales | FALSE | FALSE | 2020-05-11 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| sessioninfo | sessioninfo | 1.1.1 | 1.1.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/sessioninfo | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/sessioninfo | FALSE | FALSE | 2018-11-05 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| sna | sna | 2.6 | 2.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/sna | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/sna | TRUE | FALSE | 2020-10-06 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| spam | spam | 2.6.0 | 2.6-0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/spam | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/spam | FALSE | FALSE | 2020-12-14 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| statnet.common | statnet.common | 4.4.1 | 4.4.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/statnet.common | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/statnet.common | TRUE | FALSE | 2020-10-03 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| stringi | stringi | 1.5.3 | 1.5.3 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/stringi | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/stringi | FALSE | FALSE | 2020-09-09 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| stringr | stringr | 1.4.0 | 1.4.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/stringr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/stringr | FALSE | FALSE | 2019-02-10 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| SummarizedExperiment | SummarizedExperiment | 1.20.0 | 1.20.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/SummarizedExperiment | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/SummarizedExperiment | TRUE | FALSE | 2020-10-27 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| survival | survival | 3.2.7 | 3.2-7 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/survival | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/survival | TRUE | FALSE | 2020-09-28 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| testthat | testthat | 3.0.1 | 3.0.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/testthat | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/testthat | FALSE | FALSE | 2020-12-17 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| tibble | tibble | 3.0.6 | 3.0.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/tibble | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/tibble | FALSE | FALSE | 2021-01-29 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| tidyr | tidyr | 1.1.2 | 1.1.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/tidyr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/tidyr | FALSE | FALSE | 2020-08-27 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| tidyselect | tidyselect | 1.1.0 | 1.1.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/tidyselect | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/tidyselect | FALSE | FALSE | 2020-05-11 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| usethis | usethis | 2.0.1 | 2.0.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/usethis | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/usethis | FALSE | FALSE | 2021-02-10 | CRAN (R 4.0.3) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| vctrs | vctrs | 0.3.6 | 0.3.6 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/vctrs | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/vctrs | FALSE | FALSE | 2020-12-17 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| vegan | vegan | 2.5.7 | 2.5-7 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/vegan | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/vegan | TRUE | FALSE | 2020-11-28 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| viridisLite | viridisLite | 0.3.0 | 0.3.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/viridisLite | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/viridisLite | FALSE | FALSE | 2018-02-01 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| webshot | webshot | 0.5.2 | 0.5.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/webshot | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/webshot | FALSE | FALSE | 2019-11-22 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| withr | withr | 2.4.1 | 2.4.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/withr | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/withr | FALSE | FALSE | 2021-01-26 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| xfun | xfun | 0.20 | 0.20 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/xfun | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/xfun | FALSE | FALSE | 2021-01-06 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| XML | XML | 3.99.0.5 | 3.99-0.5 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/XML | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/XML | FALSE | FALSE | 2020-07-23 | CRAN (R 4.0.2) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| xml2 | xml2 | 1.3.2 | 1.3.2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/xml2 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/xml2 | FALSE | FALSE | 2020-04-23 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| xtable | xtable | 1.8.4 | 1.8-4 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/xtable | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/xtable | FALSE | FALSE | 2019-04-21 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| XVector | XVector | 0.30.0 | 0.30.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector | FALSE | FALSE | 2020-10-28 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| yaml | yaml | 2.2.1 | 2.2.1 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/yaml | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/yaml | FALSE | FALSE | 2020-02-01 | CRAN (R 4.0.0) | /Library/Frameworks/R.framework/Versions/4.0/Resources/library | |
| zlibbioc | zlibbioc | 1.36.0 | 1.36.0 | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc | /Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc | FALSE | FALSE | 2020-10-28 | Bioconductor | /Library/Frameworks/R.framework/Versions/4.0/Resources/library |