Package: rgsepd 1.39.0

Karl Stamm

rgsepd: Gene Set Enrichment / Projection Displays

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

Authors:Karl Stamm

rgsepd_1.39.0.tar.gz
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rgsepd.pdf |rgsepd.html✨
rgsepd/json (API)
NEWS

# Install 'rgsepd' in R:

install.packages('rgsepd', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

IlluminaBodymap - Sample RNA-Seq Counts data
IlluminaBodymapMeta - Metadata table for the included sample data

On BioConductor:rgsepd-1.39.0(bioc 3.21)rgsepd-1.38.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology software differentialexpression genesetenrichment rnaseq

3.30 score 10 scripts 226 downloads 1 mentions 14 exports 118 dependencies

Last updated 4 months agofrom:42b2653cb2. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 22 2025
R-4.5-win	NOTE	Jan 22 2025
R-4.5-linux	NOTE	Jan 22 2025
R-4.4-win	NOTE	Jan 22 2025
R-4.4-mac	NOTE	Jan 22 2025
R-4.3-win	NOTE	Jan 22 2025
R-4.3-mac	NOTE	Jan 22 2025

Exports:DisplayName ExtractProjection GSEPD_ChangeConditions GSEPD_ChangeOutput GSEPD_DEGHeatmap GSEPD_Export_DESeq GSEPD_Heatmap GSEPD_INIT GSEPD_PCA_Plot GSEPD_PCA_Spec GSEPD_Process GSEPD_ProcessAll GSEPD_PullDEG Name_to_RefSeq

Dependencies:abind AnnotationDbi askpass BH BiasedUrn Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem caTools cli codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 digest dplyr fansi farver fastmap filelock formatR futile.logger futile.options geneLenDataBase generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue GO.db goseq gplots gtable gtools hms httr httr2 IRanges isoband jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl org.Hs.eg.db pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

An Introduction to the rgsepd package

Rendered fromrgsepd.Rnwusingknitr::knitron Jan 22 2025.

Last update: 2022-03-22
Started: 2014-12-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
R/Gene Set Enrichment and Projection Displays	rgsepd-package rgsepd
DisplayName	DisplayName
ExtractProjection	ExtractProjection
GSEPD_ChangeConditions	GSEPD_ChangeConditions
GSEPD_ChangeOutput	GSEPD_ChangeOutput
Differentially Expressed Genes Heatmap	GSEPD_DEGHeatmap
Export DESeqDataSet object	GSEPD_Export_DESeq
GSEPD_Heatmap	GSEPD_Heatmap
Initialization	GSEPD_INIT
Principle Components Analysis figure generation	GSEPD_PCA_Plot
Specialized PCA Plot	GSEPD_PCA_Spec
Processing	GSEPD_Process
GSEPD_ProcessAll	GSEPD_ProcessAll
Pull Differentially Expressed Genes	GSEPD_PullDEG
Sample RNA-Seq Counts data	IlluminaBodymap
Metadata table for the included sample data	IlluminaBodymapMeta
Name to RefSeq	Name_to_RefSeq