Functions for differential expression analysis of read counts from
messenger RNA (mRNA) sequencing (RNA-Seq) data or micro RNA (miRNA) expression
values generated by the Comprehensive Analysis Pipeline for microRNA Sequencing
(CAP-miRSeq) 'expression_reports.sh' script. The workflow follows the
'edgeR'-'limma' expression data analysis pipeline providing options for different
approaches, such as "pure" 'edgeR', voom or paired samples. The functions in the
package generate text files with differential expression lists, optionally
annotated with information from 'biomart', expression summary plots as well as
several quality control (QC) plots. The main function, diffExpr(), is a
convenience wrapper performing all steps automatically based on sensible defaults.
Methods are described in Robinson, McCarthy and Smyth (2010)
<doi:10.1093/bioinformatics/btp616>, Ritchie et al. (2015)
<doi:10.1093/nar/gkv007>, Law et al. (2014) <doi:10.1186/gb-2014-15-2-r29> and
Sun et al. (2014) <doi:10.1186/1471-2164-15-423>.
| Version: |
0.6-3 |
| Depends: |
R (≥ 4.0.0) |
| Imports: |
plyr, ggplot2, edgeR, limma, RColorBrewer, convertid (≥
0.3.4), pheatmap, ggrepel, data.table, magrittr, methods, Hmisc, ltm, openxlsx, purrr, dplyr, venn, VennDiagram, grid, scales |
| Suggests: |
testthat (≥ 3.0.0), withr, futile.logger, rappdirs, knitr, quarto, dendextend, rmarkdown, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, clusterProfiler, gprofiler2, topGO, igraph, scatterplot3d, readxl, WriteXLS, biomaRt |
| Published: |
2026-08-30 |
| DOI: |
10.32614/CRAN.package.diffwrap (may not be active yet) |
| Author: |
Vidal Fey [aut, cre],
Meeri Pekkarinen [aut],
Reija Hieta [aut],
Bogdan Iancu [aut],
Adrien Janssens [aut] |
| Maintainer: |
Vidal Fey <vidal.fey at gmail.com> |
| License: |
GPL-3 |
| NeedsCompilation: |
no |
| CRAN checks: |
diffwrap results |