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tximeta

Bioc current

Transcript Quantification Import with Automatic Metadata

v1.30.0 · software · GPL-2
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.8 · Oct 31, 2018

Current · Requires R 4.6

1.0 In 16 of 49 releases 3.23

Description

Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

56 16 exported

Complexity

4.7 avg / 19 max

Call network

56 nodes / 97 edges

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

Call graph

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Lowest coverage

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

Code

Structure

Lines of code

5,641

Files

58

Compiled share

0%

Has compiled src

No

Language breakdown

R 3,018 (53.5%)Tests 511 (9.1%)Docs 1,040 (18.4%)Vignettes 1,072 (19%)

API

Exported functions

16

Internal functions

40

Recent export changes

v3.9−1 summarizeToGene
v3.8+7 addIds, getTximetaBFC, loadLinkedTxome +4 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.17

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

0%

Unsafe pattern score

0

Dep constraint coverage

10%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1.0

System requirements

–

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

16

First release

2019-01-11

Latest release

2026-04-28

Avg cadence

176 days

Cold removal rate

100%

Dep drift

11

LOC over versions

v3.8: 1,583 LOCv3.9: 1,828 LOCv3.10: 2,374 LOCv3.11: 3,282 LOCv3.12: 3,626 LOCv3.13: 3,672 LOCv3.14: 3,696 LOCv3.15: 3,733 LOCv3.16: 3,744 LOCv3.17: 3,754 LOCv3.18: 3,903 LOCv3.19: 3,917 LOCv3.20: 3,929 LOCv3.21: 3,973 LOCv3.22: 5,497 LOCv3.23: 5,641 LOC

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

Documentation

Documentation
READMEYes · 423 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductYesContributing guideNo
Examples that run
92%
Documented parameters
98%
Return-value docs
100%
References docs
6%

Topics

Software › WorkflowStep › Annotation
Software › BiologicalQuestion › GenomeAnnotation
Software › Infrastructure › DataImport
Software › WorkflowStep › Preprocessing
Software › Technology › Sequencing › RNASeq
Software › Technology › Sequencing › LongRead
Software › Technology › SingleCell
Software › ResearchField › Transcriptomics
Software › AssayDomain › Transcription
Software › AssayDomain › GeneExpression
Software › ResearchField › FunctionalGenomics
ExperimentData › ReproducibleResearch
Software › WorkflowStep › ReportWriting
Software › ResearchField › Immunology › ImmunoOncology

Depended on by (5)

Bioconductor (5)

DESeq2 fishpond IsoformSwitchAnalyzeR fluentGenomics rnaseqGene

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