tximportData
Bioc currenttximportData
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. alevin example output is also included. Forr details on version numbers, sample information, and details on calls, see the package vignette.
None published for Bioconductor
Call graph
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
205
Files
371
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
0
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
–
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-15
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- No help pages
- Examples that run
- no examples
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- not tracked
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| abundance | data.frame | 200,401 × 5 | No other package |
| samples | data.frame | 6 × 6 | No other package |
| samples_extended | data.frame | 6 × 35 | No other package |
| sgnex_h9_rep2.ambig_info | data.frame | 423,044 × 3 | No other package |
| sgnex_h9_rep3.ambig_info | data.frame | 423,044 × 3 | No other package |
| sgnex_h9_rep4.ambig_info | data.frame | 423,044 × 3 | No other package |
| tx2gene | data.frame | 48,006 × 2 | No other package |
| tx2gene.ensembl.v87 | data.frame | 198,002 × 2 | No other package |
| tx2gene.gencode.v27 | data.frame | 200,401 × 2 | No other package |
| tx2gene_alevin | data.frame | 142,374 × 2 | No other package |
| tx2gene_tasic | data.frame | 144,524 × 3 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (8)
People (from the free-text Author field)
Cite
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Run in R for the authors' preferred citation:
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