Package: fishpond 2.19.0

Michael Love

fishpond: Fishpond: downstream methods and tools for expression data

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.

Authors:Anqi Zhu [aut, ctb], Michael Love [aut, cre], Avi Srivastava [aut, ctb], Rob Patro [aut, ctb], Joseph Ibrahim [aut, ctb], Hirak Sarkar [ctb], Euphy Wu [ctb], Noor Pratap Singh [ctb], Scott Van Buren [ctb], Dongze He [ctb], Steve Lianoglou [ctb], Wes Wilson [ctb], Jeroen Gilis [ctb]

fishpond_2.19.0.tar.gz
fishpond_2.19.0.zip(r-4.7)fishpond_2.19.0.zip(r-4.6)fishpond_2.19.0.zip(r-4.5)
fishpond_2.19.0.tgz(r-4.6-any)fishpond_2.19.0.tgz(r-4.5-any)
fishpond_2.19.0.tar.gz(r-4.7-any)fishpond_2.19.0.tar.gz(r-4.6-any)
fishpond_2.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
fishpond/json (API)
NEWS

# Install 'fishpond' in R:
install.packages('fishpond', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thelovelab/fishpond/issues

Pkgdown/docs site:https://thelovelab.github.io

On BioConductor:fishpond-2.19.0(bioc 3.24)fishpond-2.18.0(bioc 3.23)

sequencingrnaseqgeneexpressiontranscriptionnormalizationregressionmultiplecomparisonbatcheffectvisualizationdifferentialexpressiondifferentialsplicingalternativesplicingsinglecellbioconductorgene-expressiongenomicssalmonscrnaseqstatisticstranscriptomics

8.06 score 32 stars 225 scripts 832 downloads 1 mentions 21 exports 45 dependencies

Last updated from:74b16838ad. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR336
linux-devel-x86_64NOTE499
source / vignettesOK565
linux-release-x86_64NOTE454
macos-release-arm64NOTE309
macos-oldrel-arm64NOTE235
windows-develNOTE348
windows-releaseNOTE362
windows-oldrelNOTE300
wasm-releaseOK251

Exports:addStatsFromCSValevinECcomputeInfRVdeswishgetTraceimportAllelicCountsisoformProportionslabelKeeploadFrymakeInfRepsmakeSimSwishDatamakeTx2TssminiSwishplotAllelicGeneplotAllelicHeatmapplotInfRepsplotMASwishsalmonECscaleInfRepssplitSwishswish

Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggplot2gluegtablegtoolsIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsplyrqvalueR6RColorBrewerRcppreshape2rlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentsvMiscvctrsviridisLitewithrXVector

Swish: differential expression accounting for inferential uncertainty

Rendered fromswish.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-08-19
Started: 2019-08-03

SEESAW - Allelic expression analysis with Salmon and Swish

Rendered fromallelic.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-04-19
Started: 2022-02-06