alpine: alpine
Version 1.2.0

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

AuthorMichael Love, Rafael Irizarry
Bioconductor views AlternativeSplicing BatchEffect Coverage DifferentialSplicing GeneExpression Normalization QualityControl RNASeq Sequencing Transcription Visualization
Date of publicationNone
MaintainerMichael Love <michaelisaiahlove@gmail.com>
LicenseGPL (>=2)
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("alpine")

Getting started

Package overview
README.md

Popular man pages

buildFragtypes: Build fragment types from exons
getReadLength: Get read length
normalizeDESeq: DESeq median ratio normalization for matrix
plotFragLen: Plot fragment length distribution 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
See all...

All man pages Function index File listing

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

Functions

addVLMMBias Source code
alphafun Source code
alpine-package Man page
alpineFlag Source code
buildFragtypes Man page Source code
calcVLMMBias Source code
ebt.fit Man page
ebt.theta Man page
endRight Source code
estimateAbundance Man page Source code
extractAlpine Man page Source code
extractRes Source code
fitBiasModels Man page Source code
fitVLMM Source code
fitpar Man page
fitpar.small Man page
gaToReadsOnTx Source code
genes.theta Man page
genomeToTx Source code
getFPBP Source code
getFragmentWidths Man page Source code
getKmerFreqs Source code
getLogLambda Source code
getPositionalKmerFreqs Source code
getPositionalObsOverExp Source code
getReadLength Man page Source code
incidenceMat Source code
mapTxToGenome Source code
matchReadsToFraglist Source code
matchToDensity Source code
mergeGenes Man page Source code
namesToModels Source code
normalizeDESeq Man page Source code
plotFragLen Man page Source code
plotGC Man page Source code
plotGRL Man page Source code
plotOrder0 Man page Source code
plotOrder1 Man page Source code
plotOrder2 Man page Source code
plotRelPos Man page Source code
predictCoverage Man page Source code
preprocessedData Man page
readGAlignAlpine Source code
res Man page
runEM Source code
splitGenesAcrossChroms Man page Source code
splitLongGenes Man page Source code
startLeft Source code
subsetAndWeightFraglist Source code
txToExon Source code
txToGenome Source code
txdf.theta Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/core.R
R/data.R
R/estimate_abundance.R
R/fit_bias.R
R/helper.R
R/plots.R
R/predict.R
R/vlmm.R
README.md
build
build/vignette.rds
data
data/preprocessedData.rda
inst
inst/CITATION
inst/doc
inst/doc/alpine.R
inst/doc/alpine.Rmd
inst/doc/alpine.html
man
man/alpine-package.Rd
man/buildFragtypes.Rd
man/estimateAbundance.Rd
man/extractAlpine.Rd
man/fitBiasModels.Rd
man/getFragmentWidths.Rd
man/getReadLength.Rd
man/mergeGenes.Rd
man/normalizeDESeq.Rd
man/plotFragLen.Rd
man/plotGC.Rd
man/plotGRL.Rd
man/plotOrder0.Rd
man/plotRelPos.Rd
man/predictCoverage.Rd
man/preprocessedData.Rd
man/splitGenesAcrossChroms.Rd
man/splitLongGenes.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_alpine.R
vignettes
vignettes/alpine.Rmd
alpine documentation built on May 20, 2017, 10:34 p.m.

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