chipseqDB
Bioc currentA Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data
Release Lineage
Entered 3.2 · Oct 14, 2015
Current · Requires R 4.6
Description
Describes a computational workflow for performing a DB analysis with sliding windows. The aim is to facilitate the practical implementation of window-based DB analyses by providing detailed code and expected output. The workflow described here applies to any ChIP-seq experiment with multiple experimental conditions and multiple biological samples in one or more of the conditions. It detects and summarizes DB regions between conditions in a de novo manner, i.e., without making any prior assumptions about the location or width of bound regions. Detected regions are then annotated according to their proximity to genes.
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Code
Structure
Lines of code
440
Files
8
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
–
Internal functions
0
Testing & CI
Has tests
No
Test-to-code ratio
–
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
22
First release
2015-10-13
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
26
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Topics
People
- Aaron Lun author maintainer
- Gordon Smyth author
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