rnaseqGene
Bioc currentRNA-seq workflow: gene-level exploratory analysis and differential expression
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.
None published for Bioconductor
Call graph
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
2,824
Files
4
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
–
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
–
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
4.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.3.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
24
First release
2014-10-13
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
32
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- No help pages
- Examples that run
- no examples
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- not tracked
Repository practices
Checks run against github.com/thelovelab/rnaseqgene on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Topics
People
- Michael Love author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("rnaseqGene")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.12688/f1000research.7035.2.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.