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DESCRIPTION
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DESCRIPTION
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Package: HTSanalyzeR2
Type: Package
Title: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data
Version: 0.99.19
Author: Lina ZHU <zhulina0609@gmail.com>, Feng GAO <gaofeng21cn@gmail.com>,
Xiupei MEI <meixiupei@gmail.com>, Xin Wang <xinwang2hms@gmail.com>
Maintainer: Lina ZHU <zhulina0609@gmail.com>
Description: This package provides gene set analysis, enriched subnetwork analyses and
'Time-series' functional analysis for various preprocessed high-throughput
data generated either by CRISPR screening, RNA-seq, micro-array or RNAi in a unified workflow.
The over-representation analysis is based on hypergeometric test and the
enrichment analysis is based on the GSEA algorithm published by
(Subramanian et al.PNAS 2005). The network analysis could identify the enriched
subnetworks based on the algorithms from BioNet package(Beisser et al., Bioinformatics 2010).
A pipeline function is provided for CRISPR data preprocessed by MAGeCK,
which is seamless linked with MAGeCK. Time series data analysis could also be
performed for better mutual comparison. Finally, a dynamic shiny report could be
generated encompassing all the results, allowing users to modify the visualization
part and download results in different formats.
License: Artistic-2.0
LazyData: TRUE
RoxygenNote: 7.1.1
Encoding: UTF-8
Imports:
GO.db,
cellHTS2,
Rcpp,
foreach,
stringr,
igraph,
BioNet,
DT,
shiny,
shinydashboard,
colourpicker,
KEGGREST,
data.table,
htmlwidgets,
methods,
RankProd,
AnnotationDbi,
graphics,
grDevices,
stats,
utils,
BiocParallel,
fgsea,
msigdbr
Collate:
'utils.R'
'class_union.R'
'Batch_class.R'
'HTSanalyzeR2.R'
'HTSanalyzeR2Pipe.R'
'HTSanalyzeR4MAGeCK.R'
'RcppExports.R'
'nwa_class.R'
'gsca_class.R'
'accessor.R'
'd3plot.R'
'data.R'
'gscaTS.R'
'gsca_analyze.R'
'gsca_enrichmap.R'
'gsca_load_genesets.R'
'gsca_preprocess.R'
'gsca_report.R'
'gsca_summarize.R'
'gsca_view.R'
'nwaTS.R'
'nwa_analyze.R'
'nwa_preprocess.R'
'nwa_report.R'
'nwa_summarize.R'
'nwa_view.R'
'stat_test.R'
'zzz.R'
LinkingTo: Rcpp
Suggests:
BiocStyle,
rmarkdown,
testthat,
knitr,
org.Hs.eg.db,
doParallel,
Biobase,
limma,
TxDb.Hsapiens.UCSC.hg19.knownGene
VignetteBuilder: knitr
Depends: R(>= 3.5)
biocViews: GeneSetEnrichment, NetworkEnrichment, TimeCourse,
GeneExpression, GO, KEGG, CRISPR