Package: yarn 1.39.0

Joseph N Paulson

yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

Authors:Joseph N Paulson [aut, cre], Cho-Yi Chen [aut], Camila Lopes-Ramos [aut], Marieke Kuijjer [aut], John Platig [aut], Abhijeet Sonawane [aut], Maud Fagny [aut], Kimberly Glass [aut], John Quackenbush [aut]

yarn_1.39.0.tar.gz
yarn_1.39.0.zip(r-4.7)yarn_1.39.0.zip(r-4.6)yarn_1.39.0.zip(r-4.5)
yarn_1.39.0.tgz(r-4.6-any)yarn_1.39.0.tgz(r-4.5-any)
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yarn_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
yarn/json (API)
NEWS

# Install 'yarn' in R:
install.packages('yarn', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • bladder - Bladder RNA-seq data from the GTEx consortium
  • skin - Skin RNA-seq data from the GTEx consortium

On BioConductor:yarn-1.39.0(bioc 3.24)yarn-1.38.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarequalitycontrolgeneexpressionsequencingpreprocessingnormalizationannotationvisualizationclustering

4.56 score 36 scripts 568 downloads 12 exports 155 dependencies

Last updated from:57fc2daa52. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING244
linux-devel-x86_64ERROR552
source / vignettesOK343
linux-release-x86_64ERROR544
macos-release-arm64ERROR236
macos-oldrel-arm64ERROR272
windows-develERROR530
windows-releaseERROR475
windows-oldrelERROR472
wasm-releaseOK184

Exports:annotateFromBiomartcheckMisAnnotationcheckTissuesToMergedownloadGTExfilterGenesfilterLowGenesfilterMissingGenesfilterSamplesnormalizeTissueAwareplotCMDSplotDensityplotHeatmap

Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbitbit64bitopsblobbumphuntercachemcaToolscigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoParalleldoRNGdownloaderdplyredgeRfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgtablegtoolsh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogquantroR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryaml

YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

Rendered fromyarn.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2018-08-30
Started: 2016-10-17