csawUsersGuide
Bioc currentcsaw User's Guide
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
A user's guide for the csaw package for detecting differentially bound regions in ChIP-seq data. Describes how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.
None published for Bioconductor
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Code
Structure
Lines of code
14
Files
3
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
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Docs
Roxygen coverage
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Health & Security signals
Informational signals; not verdicts.
on.exit coverage
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Unsafe pattern score
0
Dep constraint coverage
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Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
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C++ standard
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License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
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
- 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
- User's guide PDF
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.
Topics
People
- Aaron Lun author maintainer
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