icetea
Bioc currentIntegrating Cap Enrichment with Transcript Expression Analysis
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
27 5 exported
Complexity
2.4 avg / 11 max
Call network
27 nodes / 12 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
4,577
Files
93
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
22
Recent export changes
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
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2019-01-04
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 35
- Examples that run
- 82%14 run in a plain check · 3 never run
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/vivekbhr/icetea on 2026-10-22.
GitHub Pages site last deployed 2020-06-02
Datasets
Topics
People
- Vivek Bhardwaj author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("icetea")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 v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.