UMI4Cats

Bioc current

UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

v1.22.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.12 · Oct 28, 2020

Current · Requires R 4.6

1.0 In 12 of 49 releases 3.23

Description

UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

59 33 exported

Complexity

3.1 avg / 15 max

Call network

59 nodes / 68 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

7,616

Files

124

Compiled share

Has compiled src

Language breakdown

R 4,408 (57.9%)Tests 116 (1.5%)Docs 2,457 (32.3%)Vignettes 635 (8.3%)

API

Exported functions

Internal functions

Recent export changes

v3.22+1 .UMI4C −1 %>%

Testing & CI

Has tests

Yes

Test-to-code ratio

0.03

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

Unsafe pattern score

Dep constraint coverage

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

First release

2020-12-29

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

100%

Dep drift

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 154 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductYesContributing guideYes

Examples that run: 94%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Topics

Software › WorkflowStep › QualityControl

Software › WorkflowStep › Preprocessing

Software › WorkflowStep › Alignment

Software › WorkflowStep › Normalization

Software › WorkflowStep › Visualization

Software › Technology › Sequencing

Software › BiologicalQuestion › Coverage

People

Mireia Ramos-Rodriguez author maintainer
Lorenzo Pasquali author
Marc Subirana-Granes author

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