Package: fishpond 2.19.2

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_2.19.2.tar.gz
fishpond_2.19.2.zip(r-4.7-any)fishpond_2.19.2.zip(r-4.6-any)fishpond_2.19.2.zip(r-4.5-any)
fishpond_2.19.2.tgz(r-4.6-any)fishpond_2.19.2.tgz(r-4.5-any)
fishpond_2.19.2.tar.gz(r-4.7-any)fishpond_2.19.2.tar.gz(r-4.6-any)
fishpond_2.19.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fishpond/json (API)

# 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-2.19.2(bioc 3.24)fishpond-2.18.0(bioc 3.23)

sequencingrnaseqgeneexpressiontranscriptionnormalizationregressionmultiplecomparisonbatcheffectvisualizationdifferentialexpressiondifferentialsplicingalternativesplicingsinglecellbioconductorgene-expressiongenomicssalmonscrnaseqstatisticstranscriptomics

8.06 score 33 stars 292 scripts 1.5k downloads 1 mentions 21 exports 45 dependencies

Last updated from:c706e65af8. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR257
linux-develNOTE581
source / vignettesOK438
linux-releaseNOTE488
macos-releaseNOTE256
macos-oldrelNOTE273
windows-develNOTE310
windows-releaseNOTE318
windows-oldrelNOTE302
wasm-releaseOK209

Exports:addStatsFromCSValevinECcomputeInfRVdeswishgetTraceimportAllelicCountsisoformProportionslabelKeeploadFrymakeInfRepsmakeSimSwishDatamakeTx2TssminiSwishplotAllelicGeneplotAllelicHeatmapplotInfRepsplotMASwishsalmonECscaleInfRepssplitSwishswish

Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggplot2gluegtablegtoolsIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsplyrqvalueR6RColorBrewerRcppreshape2rlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentsvMiscvctrsviridisLitewithrXVector

Swish: differential expression accounting for inferential uncertainty
The Swish method | Quick start | Macrophage stimulation experiment | Data import | Read in the column data from CSV | Add a column pointing to your files | Read in quants with tximeta | Differential transcript expression | Running Swish at the transcript level | Plotting results | Differential gene expression | Running Swish at the gene level | Plotting gene results | Differential transcript usage | Interaction designs | Condition and secondary covariates | Create and check paired samples | Swish for interaction effects | Plotting interaction results | Allelic expression analysis | Correlation test | alevin scRNA-seq | Further details | Analysis types supported by Swish | Accounting for continuous variables | Structure of tximeta output | Plotting q-values over statistics | Plotting InfRV | Salmon in alignment mode, how to use tximeta | Permutation schemes for interactions | Session information | References
Rendered fromswish.Rmdusingknitr::rmarkdown

Last update: 2026-09-28
Started: 2019-08-03

SEESAW - Allelic expression analysis with Salmon and Swish
Introduction | Quick start | Method overview | Linking transcripts to TSS | Importing allelic counts | Filtering features | Global allelic imbalance | Plotting results | Differential allelic imbalance | Dynamic allelic imbalance | More complex designs | Further questions | Session info | References
Rendered fromallelic.Rmdusingknitr::rmarkdown

Last update: 2025-01-02
Started: 2022-02-06