BP4RNAseq
Bioc currentA babysitter's package for reproducible RNA-seq analysis
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
An automated pipe for reproducible RNA-seq analysis with the minimal efforts from researchers. The package can process bulk RNA-seq data and single-cell RNA-seq data. You can only provide the taxa name and the accession id of RNA-seq data deposited in the National Center for Biotechnology Information (NCBI). After a cup of tea or longer, you will get formated gene expression data as gene count and transcript count based on both alignment-based and alignment-free workflows.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
27 13 exported
Complexity
6.7 avg / 19 max
Call network
27 nodes / 40 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
1,902
Files
48
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
14
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
10 externalUNIX, SRA Toolkit=2.10.3, Entrez Direct=13.3, FastQC=v0.11.9, Cutadapt=2.10, datasets, SAMtools=1.9, HISAT2=2.2.0, StringTie=2.1.1, Salmon=1.2.1
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 13
- Examples that run
- 92%12 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- BP4RNAseq vignette HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| test_gene_alignment_based_quantification | data.frame | 4 × 3 | No other package |
| test_gene_alignment_free_quantification | data.frame | 4 × 3 | No other package |
| test_transcript_alignment_based_quantification | data.frame | 5 × 3 | No other package |
| test_transcript_alignment_free_quantification | data.frame | 4 × 3 | No other package |
Topics
People
- Shanwen Sun maintainer author
- Lei Xu author
- Quan Zou author
Cite
Cite this package
Run in R for the authors' entry:
citation("BP4RNAseq")The package provides a citation file, so citation() returns the authors' own entry.
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.