alpine: alpine

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Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.

Author
Michael Love, Rafael Irizarry
Date of publication
None
Maintainer
Michael Love <michaelisaiahlove@gmail.com>
License
GPL (>=2)
Version
1.0.0

View on Bioconductor

Man pages

alpine-package
alpine: bias corrected transcript abundance estimation
buildFragtypes
Build fragment types from exons
estimateAbundance
Estimate bias-corrected transcript abundances (FPKM)
extractAlpine
Extract results from estimateAbundance run across genes
fitBiasModels
Fit bias models over single-isoform genes
getFragmentWidths
Get fragment widths
getReadLength
Get read length
mergeGenes
Merge overlapping "genes" into gene clusters
normalizeDESeq
DESeq median ratio normalization for matrix
plotFragLen
Plot fragment length distribution over samples
plotGC
Plot the fragment GC bias over samples
plotGRL
Simple segments plot for GRangesList
plotOrder0
Plot parameters of the variable length Markov model (VLMM)...
plotRelPos
Plot relative position bias over samples
predictCoverage
Predict coverage for a single-isoform gene
preprocessedData
Preprocessed data for vignettes and examples
splitGenesAcrossChroms
Split genes that have isoforms across chromosomes
splitLongGenes
Split very long genes

Files in this package

alpine/DESCRIPTION
alpine/NAMESPACE
alpine/NEWS
alpine/R
alpine/R/core.R
alpine/R/data.R
alpine/R/estimate_abundance.R
alpine/R/fit_bias.R
alpine/R/helper.R
alpine/R/plots.R
alpine/R/predict.R
alpine/R/vlmm.R
alpine/README.md
alpine/build
alpine/build/vignette.rds
alpine/data
alpine/data/preprocessedData.rda
alpine/inst
alpine/inst/doc
alpine/inst/doc/alpine.R
alpine/inst/doc/alpine.Rmd
alpine/inst/doc/alpine.html
alpine/man
alpine/man/alpine-package.Rd
alpine/man/buildFragtypes.Rd
alpine/man/estimateAbundance.Rd
alpine/man/extractAlpine.Rd
alpine/man/fitBiasModels.Rd
alpine/man/getFragmentWidths.Rd
alpine/man/getReadLength.Rd
alpine/man/mergeGenes.Rd
alpine/man/normalizeDESeq.Rd
alpine/man/plotFragLen.Rd
alpine/man/plotGC.Rd
alpine/man/plotGRL.Rd
alpine/man/plotOrder0.Rd
alpine/man/plotRelPos.Rd
alpine/man/predictCoverage.Rd
alpine/man/preprocessedData.Rd
alpine/man/splitGenesAcrossChroms.Rd
alpine/man/splitLongGenes.Rd
alpine/tests
alpine/tests/testthat
alpine/tests/testthat.R
alpine/tests/testthat/test_alpine.R
alpine/vignettes
alpine/vignettes/alpine.Rmd