Package: yarn 1.33.0

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]

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yarn.pdf |yarn.html
yarn/json (API)
NEWS

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

Peer review:

Datasets:
  • bladder - Bladder RNA-seq data from the GTEx consortium
  • skin - Skin RNA-seq data from the GTEx consortium

On BioConductor:yarn-1.33.0(bioc 3.21)yarn-1.32.0(bioc 3.20)

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

softwarequalitycontrolgeneexpressionsequencingpreprocessingnormalizationannotationvisualizationclustering

4.97 score 1 packages 31 scripts 340 downloads 12 exports 157 dependencies

Last updated 2 months agofrom:7e48450e3f. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winOKNov 30 2024
R-4.5-linuxOKNov 30 2024
R-4.4-winOKNov 30 2024
R-4.4-macOKNov 30 2024
R-4.3-winOKNov 30 2024
R-4.3-macOKNov 30 2024

Exports:annotateFromBiomartcheckMisAnnotationcheckTissuesToMergedownloadGTExfilterGenesfilterLowGenesfilterMissingGenesfilterSamplesnormalizeTissueAwareplotCMDSplotDensityplotHeatmap

Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbumphuntercachemcaToolsclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdoParalleldoRNGdownloaderdplyredgeRfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgtablegtoolsHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminfimulttestmunsellnlmenor1mixopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogquantroR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryamlzlibbioc

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

Rendered fromyarn.Rmdusingknitr::rmarkdownon Nov 30 2024.

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