Differential Expression Analysis of RNA-Seq Data
Overview
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.
Install
Health
ERRORtestsr-oldrel-macos-x86_64
Running ‘testthat.R’ [13s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(diffwrap)
>
> test_check("diffwrap")
@ -- STARTUP CHECKS --
@ -- PREPARING RUN ENVIRONMENT --
@ -- STARTUP CHECKS --
@ -- PREPARING RUN ENVIRONMENT --
Saving _problems/test-fit-102.R
[ FAIL 1 | WARN 0 | SKIP 12 | PASS 175 ]
══ Skipped tests (12) ══════════════════════════════════════════════════════════
• On CRAN (11): 'test-bugfixes.R:108:3', 'test-bugfixes.R:192:3',
'test-bugfixes.R:224:3', 'test-diffExpr-e2e.R:27:3',
'test-diffExpr-e2e.R:69:3', 'test-diffExpr-e2e.R:95:3',
'test-diffExpr-e2e.R:116:3', 'test-enrichment.R:69:3',
'test-enrichment.R:92:3', 'test-enrichment.R:122:3',
'test-enrichment.R:142:3'
• convertId2 unavailable: The Bioconductor package 'org.Mm.eg.db' is required
for this function. (1): 'test-bugfixes.R:98:13'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-fit.R:102:3'): the paired fit removes the subject effect ─────
Expected `median(fit_p$d2$tagwise.dispersion)` < `median(fit_u$d2$tagwise.dispersion)`.
Actual comparison: 0.1538 >= 0.1512
Difference: 0.0025 >= 0
[ FAIL 1 | WARN 0 | SKIP 12 | PASS 175 ]
Error:
! Test failures.
Execution halted- ERROR12 OK, 1 ERRORNow
- ERROR6 OK, 1 ERROR2026-08-31
Documentation
- Help pages
- 48 (4 internal)includes a package overview page
- Examples that run
- 42%15 run in a plain check · 21 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 97%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Downloads
Dependencies
Installing diffwrap adds 85 packages (45 with compiled code, 63 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 5 more not on CRAN are not measured.
CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.
- lambda.r through VennDiagram → futile.loggerdeadline passed Oct 12
Code & Tests
Datasets
People & History
- 0.6-3Latest2026-08-30 · current release
- RR 4.6.0 released · 2026-04-24
Package metadata
- First published
- 2026-08-30
- Total releases
- 1 / 1 yrs
- License
- GPL-3 OSI
- Minimum R
- ≥ 4.0.0
- Bundled data
- 7.4 KB / 2 files
- Download size
- 810 KB
Cite
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Run in R for the authors' preferred citation:
citation("diffwrap")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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