generegulation
Bioc currentFinding Candidate Binding Sites for Known Transcription Factors via Sequence Matching
Release Lineage
Entered 2.12 · Apr 4, 2013
Current · Requires R 4.6
Description
The binding of transcription factor proteins (TFs) to DNA promoter regions upstream of gene transcription start sites (TSSs) is one of the most important mechanisms by which gene expression, and thus many cellular processes, are controlled. Though in recent years many new kinds of data have become available for identifying transcription factor binding sites (TFBSs) -- ChIP-seq and DNase I hypersensitivity regions among them -- sequence matching continues to play an important role. In this workflow we demonstrate Bioconductor techniques for finding candidate TF binding sites in DNA sequence using the model organism Saccharomyces cerevisiae. The methods demonstrated here apply equally well to other organisms.
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Code
Structure
Lines of code
572
Files
7
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
0%
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
27
First release
2013-07-29
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Topics
People
- Bioconductor Package Maintainer author maintainer