Package: pairedGSEA 1.7.0

Søren Helweg Dam

pairedGSEA: Paired DGE and DGS analysis for gene set enrichment analysis

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

Authors:Søren Helweg Dam [cre, aut], Lars Rønn Olsen [aut], Kristoffer Vitting-Seerup [aut]

pairedGSEA_1.7.0.tar.gz
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pairedGSEA.pdf |pairedGSEA.html✨
pairedGSEA/json (API)
NEWS

# Install 'pairedGSEA' in R:

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

Bug tracker:https://github.com/shdam/pairedgsea/issues

Datasets:

example_diff_result - Output of running paired_diff on example_se.
example_gene_sets - MSigDB gene sets from humans, category C5 with ensemble gene IDs
example_ora_results - Output of running paired_ora on example_diff_result and gene sets extracted from MSigDB
example_se - A small subset of the GEO:GSE61220 data set.

On BioConductor:pairedGSEA-1.7.0(bioc 3.21)pairedGSEA-1.6.0(bioc 3.20)

differentialexpression alternativesplicing differentialsplicing geneexpression immunooncology genesetenrichment pathways rnaseq software transcription

4.48 score 2 stars 110 downloads 4 exports 117 dependencies

Last updated 25 days agofrom:e165c3665e. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	WARNING	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

Exports:paired_diff paired_ora plot_ora prepare_msigdb

Dependencies:abind aggregation annotate AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray DESeq2 DEXSeq digest dplyr edgeR fansi farver fastmap fastmatch fgsea filelock formatR futile.logger futile.options genefilter geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable hms httr httr2 hwriter IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo Rhtslib rlang Rsamtools RSQLite S4Arrays S4Vectors scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XML xml2 xtable XVector zlibbioc

User Guide

Søren Helweg Dam

Rendered fromUser-Guide.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-04-28
Started: 2022-08-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Output of running paired_diff on example_se.	example_diff_result
MSigDB gene sets from humans, category C5 with ensemble gene IDs	example_gene_sets
Output of running paired_ora on example_diff_result and gene sets extracted from MSigDB	example_ora_results
A small subset of the GEO:GSE61220 data set.	example_se
Run paired DESeq2 and DEXSeq analyses	paired_diff
Paired Over-Representation Analysis	paired_ora
Scatter plot of Over-Representation Analysis results	plot_ora
Load MSigDB and convert to names list of gene sets	prepare_msigdb