Package: yarn 1.31.0
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:
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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')) |
On BioConductor:yarn-1.31.0(bioc 3.20)yarn-1.30.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:59a1448964
Exports:annotateFromBiomartcheckMisAnnotationcheckTissuesToMergedownloadGTExfilterGenesfilterLowGenesfilterMissingGenesfilterSamplesnormalizeTissueAwareplotCMDSplotDensityplotHeatmap
Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbumphuntercachemcaToolsclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdoParalleldoRNGdownloaderdplyredgeRfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgtablegtoolsHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminfimulttestmunsellnlmenor1mixopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogquantroR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesscrimesiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate your Expression Set with biomaRt | annotateFromBiomart |
| Bladder RNA-seq data from the GTEx consortium | bladder |
| Check for wrong annotation of a sample using classical MDS and control genes. | checkMisAnnotation |
| Check tissues to merge based on gene expression profile | checkTissuesToMerge |
| Download GTEx files and turn them into ExpressionSet object | downloadGTEx |
| Extract the appropriate matrix | extractMatrix |
| Filter specific genes | filterGenes |
| Filter genes that have less than a minimum threshold CPM for a given group/tissue | filterLowGenes |
| Filter genes not expressed in any sample | filterMissingGenes |
| Filter samples | filterSamples |
| Normalize in a tissue aware context | normalizeTissueAware |
| Plot classical MDS of dataset | plotCMDS |
| Density plots of columns in a matrix | plotDensity |
| Plot heatmap of most variable genes | plotHeatmap |
| Quantile shrinkage normalization | qsmooth |
| Compute quantile statistics | qstats |
| Skin RNA-seq data from the GTEx consortium | skin |