No description, website, or topics provided.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R added more functionality in rna_visualize function Dec 10, 2018
docs
man
vignettes
.gitignore
DESCRIPTION
LICENSE
NAMESPACE minor updates Sep 16, 2018
README.md
_pkgdown.yaml
plot-functions
rnaseq.work.Rproj

README.md

R library - rnaseq.work

This library provides simple APIs for RNAseq data analysis.

Function 'rna_diff_expr'

The function rna_diff_expr() allows analysis of RNAseq data using various approaches (e.g. DESeq, DESeq2, edgeR, limma-voom, sleuth, baySeq, NOISeq, EBSeq, etc.). You just need to give the count_table and design_table in the form of data frames, and the rest will be taken care of by the function. Only DESeq2 and edgeR are implemented so far.

rna_diff_expr(count_table, design_table, method="DESeq")
rna_diff_expr(count_table, design_table, method="DESeq2")
rna_diff_expr(count_table, design_table, method="edgeR")
rna_diff_expr(count_table, design_table, method="limma-voom")
rna_diff_expr(count_table, design_table, method="sleuth")
rna_diff_expr(count_table, design_table, method="baySeq")
rna_diff_expr(count_table, design_table, method="NOISeq")
rna_diff_expr(count_table, design_table, method="EBSeq")

Function rna_visualize

The function rna_visualize() plots RNAseq-related data in various ways (e.g. histogram, boxplot, density plot, clustering, MA plot, smear plot, MDS plot, PCA plot, BCV plot, volcano plot) in both base and ggplot libraries. You just have to change the 'method' parameter to appropriate plot type.

rna_visualize(data_table, method="hist", col="treated1")
rna_visualize(data_table, method="MA", col=c("treated1", "untreated1"))
rna_visualize(data_table, method="counts", gene="gene1")
rna_visualize(data_table, method="PCA")
rna_visualize(data_table, method="MDS")
rna_visualize(data_table, method="BCV")
rna_visualize(data_table, method="smear")
rna_visualize(data_table, method="dispersions")
rna_visualize(data_table, method="sparsity")
rna_visualize(data_table, method="volcano")
rna_visualize(data_table, method="hist", lib="base", col="treated1")
rna_visualize(data_table, method="hist", lib="ggplot", col="untreated1")