Package: fishpond 2.13.0

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]

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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:https://thelovelab.github.io

On BioConductor:fishpond-2.13.0(bioc 3.21)fishpond-2.12.0(bioc 3.20)

sequencing rnaseq geneexpression transcription normalization regression multiplecomparison batcheffect visualization differentialexpression differentialsplicing alternativesplicing singlecell bioconductor gene-expression genomics salmon scrnaseq statistics transcriptomics

7.75 score 27 stars 150 scripts 600 downloads 1 mentions 21 exports 63 dependencies

Last updated 2 months agofrom:df45f798c5. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:addStatsFromCSV alevinEC computeInfRV deswish getTrace importAllelicCounts isoformProportions labelKeep loadFry makeInfReps makeSimSwishData makeTx2Tss miniSwish plotAllelicGene plotAllelicHeatmap plotInfReps plotMASwish salmonEC scaleInfReps splitSwish swish

Dependencies:abind askpass Biobase BiocGenerics cli colorspace crayon curl DelayedArray fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable gtools httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr qvalue R6 RColorBrewer Rcpp reshape2 rlang S4Arrays S4Vectors scales SingleCellExperiment SparseArray stringi stringr SummarizedExperiment svMisc sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Swish: differential expression accounting for inferential uncertainty

Rendered fromswish.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

SEESAW - Allelic expression analysis with Salmon and Swish

Rendered fromallelic.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

Help page	Topics
Fishpond: downstream methods and tools for expression data	fishpond-package
Read statistics and nulls from CSV file	addStatsFromCSV
Construct a sparse matrix of transcript compatibility counts from alevin output	alevinEC
Compute inferential relative variance (InfRV)	computeInfRV
deswish: DESeq2-apeglm With Inferential Samples Helps	deswish
Obtain a trace of inferential replicates for a sample	getTrace
Import allelic counts as a SummarizedExperiment	importAllelicCounts
Create isoform proportions from scaled data	isoformProportions
Label rows to keep based on minimal count	labelKeep
Load in data from alevin-fry USA mode	loadFry
Make pseudo-inferential replicates from mean and variance	makeInfReps
Make simulated data for swish for examples/testing	makeSimSwishData
Make a GRanges linking transcripts to TSS within gene	makeTx2Tss
Helper function for distributing Swish on a subset of data	miniSwish
Plot allelic counts in a gene context using Gviz	plotAllelicGene
Plot allelic ratio heatmap	plotAllelicHeatmap
Plot inferential replicates for a gene or transcript	plotInfReps
MA plot - log fold change over average counts	plotMASwish
Construct a sparse matrix of transcript compatibility counts from salmon output	salmonEC
Scale inferential replicate counts	scaleInfReps
Function for splitting SummarizedExperiment into separate RDS files	splitSwish
Swish method: differential expression accounting for inferential uncertainty	swish

Package: fishpond 2.13.0

fishpond: Fishpond: downstream methods and tools for expression data

Swish: differential expression accounting for inferential uncertainty

SEESAW - Allelic expression analysis with Salmon and Swish

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Help Manual

Usage by other packages (reverse dependencies)