fishpond
Bioc currentFishpond: downstream methods and tools for expression data
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
62 21 exported
Complexity
6.7 avg / 62 max
Call network
62 nodes / 71 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
8,060
Files
79
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
21
Internal functions
41
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.21
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
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
15
First release
2019-08-11
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 22includes a package overview page
- Examples that run
- 91%10 run in a plain check · 1 never run
- Exported functions with examples
- 52%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 45%
Repository practices
8 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/thelovelab/fishpond on 2026-10-18.
The R CMD check workflow runs on Linux and macOS, and on R-devel
GitHub Pages site last deployed 2026-10-01 · The repository has a site deploy workflow
pkgdown site last built 2026-10-01
Show all practicesHide 1 practice
Topics
People
- Michael Love author maintainer
- Jeroen Gilis contributor
- Dongze He contributor
- Joseph Ibrahim author contributor
- Steve Lianoglou contributor
- Rob Patro author contributor
- Noor Pratap Singh contributor
- Hirak Sarkar contributor
- Avi Srivastava author contributor
- Scott Van Buren contributor
- Wes Wilson contributor
- Euphy Wu contributor
- Anqi Zhu author contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("fishpond")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nar/gkz622.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.