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:
yarn_1.33.0.tar.gz
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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-1.33.0(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
Last updated 2 months agofrom:7e48450e3f. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 30 2024 |
R-4.5-win | OK | Nov 30 2024 |
R-4.5-linux | OK | Nov 30 2024 |
R-4.4-win | OK | Nov 30 2024 |
R-4.4-mac | OK | Nov 30 2024 |
R-4.3-win | OK | Nov 30 2024 |
R-4.3-mac | OK | Nov 30 2024 |
Exports:annotateFromBiomartcheckMisAnnotationcheckTissuesToMergedownloadGTExfilterGenesfilterLowGenesfilterMissingGenesfilterSamplesnormalizeTissueAwareplotCMDSplotDensityplotHeatmap
Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbumphuntercachemcaToolsclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdoParalleldoRNGdownloaderdplyredgeRfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgtablegtoolsHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminfimulttestmunsellnlmenor1mixopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogquantroR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.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 |