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:
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)
yarn_1.39.0.tar.gz(r-4.7-any)yarn_1.39.0.tar.gz(r-4.6-any)
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')) |
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
Last updated from:57fc2daa52. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 244 | ||
| linux-devel-x86_64 | ERROR | 552 | ||
| source / vignettes | OK | 343 | ||
| linux-release-x86_64 | ERROR | 544 | ||
| macos-release-arm64 | ERROR | 236 | ||
| macos-oldrel-arm64 | ERROR | 272 | ||
| windows-devel | ERROR | 530 | ||
| windows-release | ERROR | 475 | ||
| windows-oldrel | ERROR | 472 | ||
| wasm-release | OK | 184 |
Exports:annotateFromBiomartcheckMisAnnotationcheckTissuesToMergedownloadGTExfilterGenesfilterLowGenesfilterMissingGenesfilterSamplesnormalizeTissueAwareplotCMDSplotDensityplotHeatmap
Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbitbit64bitopsblobbumphuntercachemcaToolscigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoParalleldoRNGdownloaderdplyredgeRfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgtablegtoolsh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogquantroR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryaml
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 |