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

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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.

Author
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]
Date of publication
None
Maintainer
Joseph N Paulson <jpaulson@jimmy.harvard.edu>
License
Artistic-2.0
Version
1.0.1

View on Bioconductor

Man pages

annotateFromBiomart
Annotate your Expression Set with biomaRt
bladder
Bladder RNA-seq data from the GTEx consortium
checkMisAnnotation
Check for wrong annotation of a sample using classical MDS...
checkTissuesToMerge
Check tissues to merge based on gene expression profile
downloadGTEx
Download GTEx files and turn them into ExpressionSet object
extractMatrix
Extract the appropriate matrix
filterGenes
Filter specific genes
filterLowGenes
Filter genes that have less than a minimum threshold CPM for...
filterMissingGenes
Filter genes not expressed in any sample
filterSamples
Filter samples
normalizeTissueAware
Normalize in a tissue aware context
plotCMDS
Plot classical MDS of dataset
plotDensity
Density plots of columns in a matrix
plotHeatmap
Plot heatmap of most variable genes
qsmooth
Quantile shrinkage normalization
qstats
Compute quantile statistics
skin
Skin RNA-seq data from the GTEx consortium

Files in this package

yarn/DESCRIPTION
yarn/NAMESPACE
yarn/R
yarn/R/annotateFromBiomart.R
yarn/R/bladder-data.R
yarn/R/checkMisAnnotation.R
yarn/R/checkTissuesToMerge.R
yarn/R/downloadGTEx.R
yarn/R/extractMatrix.R
yarn/R/filterGenes.R
yarn/R/filterLowGenes.R
yarn/R/filterMissingGenes.R
yarn/R/filterSamples.R
yarn/R/normalizeTissueAware.R
yarn/R/plotCMDS.R
yarn/R/plotDensity.R
yarn/R/plotHeatmap.R
yarn/R/qsmooth.R
yarn/R/qstats.R
yarn/R/skin-data.R
yarn/README.md
yarn/build
yarn/build/vignette.rds
yarn/data
yarn/data/bladder.rdata
yarn/data/datalist
yarn/data/skin.rdata
yarn/inst
yarn/inst/NEWS
yarn/inst/doc
yarn/inst/doc/yarn.R
yarn/inst/doc/yarn.Rmd
yarn/inst/doc/yarn.pdf
yarn/man
yarn/man/annotateFromBiomart.Rd
yarn/man/bladder.Rd
yarn/man/checkMisAnnotation.Rd
yarn/man/checkTissuesToMerge.Rd
yarn/man/downloadGTEx.Rd
yarn/man/extractMatrix.Rd
yarn/man/filterGenes.Rd
yarn/man/filterLowGenes.Rd
yarn/man/filterMissingGenes.Rd
yarn/man/filterSamples.Rd
yarn/man/normalizeTissueAware.Rd
yarn/man/plotCMDS.Rd
yarn/man/plotDensity.Rd
yarn/man/plotHeatmap.Rd
yarn/man/qsmooth.Rd
yarn/man/qstats.Rd
yarn/man/skin.Rd
yarn/tests
yarn/tests/testthat
yarn/tests/testthat.R
yarn/tests/testthat/test-functions.R
yarn/vignettes
yarn/vignettes/yarn.Rmd