pasilla
Bioc currentData package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181.
None published for Bioconductor
Call graph
Open call graph →Code intelligence has not been computed for this package yet.
Code
Structure
Lines of code
246
Files
18
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
0
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
LGPL
License flags
not SPDX, not OSI
History
Versions
26
First release
2013-12-13
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
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
- 1
- Examples that run
- no examples
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 0%
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 |
|---|---|---|---|
| dxd | – | – | – |
| geneIDsinsubset | data.frame | 45 × 1 | 2 packages |
| pasilla_gene_counts | data.frame | 14,599 × 8 | 2 packages |
| pasilla_sample_annotation | data.frame | 7 × 6 | 2 packages |
| treated1fb | data.frame | 70,466 × 2 | No other package |
| treated2fb | data.frame | 70,466 × 2 | No other package |
| treated3fb | data.frame | 70,466 × 2 | No other package |
| untreated1fb | data.frame | 70,466 × 2 | No other package |
| untreated2fb | data.frame | 70,466 × 2 | No other package |
| untreated3fb | data.frame | 70,466 × 2 | No other package |
| untreated4fb | data.frame | 70,466 × 2 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (10)
People (from the free-text Author field)
Cite
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