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DESCRIPTION
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DESCRIPTION
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Package: DEbPeak
Title: DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression
Version: 1.4.0
Authors@R:
person(given = "Yabing",
family = "Song",
role = c("aut", "cre"),
email = "[email protected]")
Maintainer: Yabing Song <[email protected]>
Description: DEbPeak aims to explore, visualize, interpret multi-omics data and unravel the regulation of gene expression by
combining RNA-seq with peak-related data (eg: ChIP-seq, ATAC-seq, m6a-seq et al.). It contains nine functional panels:
Parse GEO, Quality Control (QC), Principal Component Analysis (PCA), Differential Analysis (DA), Functional Enrichment Analysis (FEA),
Integrate RNA-seq with peak-related data (support the simultaneous integration of two kinds of peak-related data),
Integrate RNA-seq with RNA-seq, Integrate peak-related data with peak-related data, Utils.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
biocViews:
RoxygenNote: 7.1.1
Depends:
R (>= 4.0.0)
Imports:
BiocManager,
circlize,
clusterProfiler (>= 3.18.1),
ComplexHeatmap,
cowplot,
DEFormats,
DESeq2,
dplyr,
edgeR,
enrichplot,
GenomicFeatures,
GenomicRanges,
ggplot2,
ggplotify,
ggrepel,
ggvenn,
ggupset,
graphics,
grDevices,
grid,
magrittr,
matrixStats,
NOISeq,
PCAtools,
plot3D,
purrr,
RColorBrewer,
reshape2,
rrcov,
rlang,
stats,
stringr,
SummarizedExperiment,
sva,
tibble,
tidyr,
utils,
ChIPseeker,
GenomeInfoDb,
viridis,
patchwork,
data.table,
scales,
ggpie,
ggpubr,
DiffBind,
parallel,
GEOquery,
Biobase,
tools,
openxlsx,
IRanges,
BiocParallel,
AnnotationDbi,
igraph,
ggnetwork,
httr,
jsonlite,
TFEA.ChIP
Suggests:
rmarkdown,
knitr,
msigdbr,
htmltools,
BiocStyle,
airway
Remotes:
YuLab-SMU/enrichplot,
YuLab-SMU/ChIPseeker
VignetteBuilder: knitr