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
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:
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✨
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-2.19.0(bioc 3.24)fishpond-2.18.0(bioc 3.23)
sequencingrnaseqgeneexpressiontranscriptionnormalizationregressionmultiplecomparisonbatcheffectvisualizationdifferentialexpressiondifferentialsplicingalternativesplicingsinglecellbioconductorgene-expressiongenomicssalmonscrnaseqstatisticstranscriptomics
Last updated from:74b16838ad. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 290 | ||
| linux-devel-x86_64 | NOTE | 459 | ||
| source / vignettes | OK | 562 | ||
| linux-release-x86_64 | NOTE | 460 | ||
| macos-release-arm64 | NOTE | 247 | ||
| macos-oldrel-arm64 | NOTE | 258 | ||
| windows-devel | NOTE | 279 | ||
| windows-release | NOTE | 366 | ||
| windows-oldrel | NOTE | 367 | ||
| wasm-release | OK | 303 |
Exports:addStatsFromCSValevinECcomputeInfRVdeswishgetTraceimportAllelicCountsisoformProportionslabelKeeploadFrymakeInfRepsmakeSimSwishDatamakeTx2TssminiSwishplotAllelicGeneplotAllelicHeatmapplotInfRepsplotMASwishsalmonECscaleInfRepssplitSwishswish
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggplot2gluegtablegtoolsIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsplyrqvalueR6RColorBrewerRcppreshape2rlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentsvMiscvctrsviridisLitewithrXVector
Swish: differential expression accounting for inferential uncertainty
Last update: 2023-08-19
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
Last update: 2023-04-19
Started: 2022-02-06
