SingleMoleculeFootprinting

Bioc current

Analysis tools for Single Molecule Footprinting (SMF) data

v2.5.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.13 · May 20, 2021

Current · Requires R 4.6

1.0 In 11 of 49 releases 3.23

Description

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

66 42 exported

Complexity

3.5 avg / 31 max

Call network

66 nodes / 67 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

6,506

Files

111

Compiled share

Has compiled src

Language breakdown

R 3,339 (51.3%)Tests 95 (1.5%)Docs 1,959 (30.1%)Vignettes 1,113 (17.1%)

API

Exported functions

Internal functions

Recent export changes

v3.21+6 FootprintCharter, PlotFootprints, Plot_FootprintCharter_SM +3 more −2 cbind.fill.Matrix, rbind.fill.Matrix

v3.20+22 Arrange_TFBSs_clusters, CollapseStrands, CollapseStrandsSM +19 more −1 SampleCorrelation

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

4.4.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

First release

2021-05-19

Latest release

2026-04-28

Avg cadence

182 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 · 201 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 55%
References docs: 0%

Topics

Software › AssayDomain › DNAMethylation

Software › BiologicalQuestion › Coverage

Software › BiologicalQuestion › NucleosomePositioning

Software › Infrastructure › DataRepresentation

Software › ResearchField › Epigenetics

Software › Technology › Sequencing › MethylSeq

Software › WorkflowStep › QualityControl

Software › Technology › Sequencing

People

Guido Barzaghi author maintainer
Arnaud Krebs author
Mike Smith contributor

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