Pasha: Preprocessing of Aligned Sequences from HTS Analyses
Version 0.99.21

Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).

Browse man pages Browse package API and functions Browse package files

AuthorRomain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Benoukraf, Pierre Cauchy, Charlene Innocenti, Pierre Ferrier, Jean-Christophe Andrau
Date of publication2016-03-18 16:23:47
MaintainerRomain Fenouil <romain.fenouil@mssm.edu>
LicenseGPL-3
Version0.99.21
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Pasha")

Man pages

AlignedData-class: Class 'AlignedData'
binVector: Divide a numeric vector in equal bins of signal
elongationEstimation: Shifting the positive strand vector and compute an overlap...
estimateElongationSize: Insert size estimation in-silico
generatePiled: Pileup reads in a numeric vector with several piling and...
getArtefactsIndexes: Identify reads implied in piles potentially considered as PCR...
mergeWigs: Merge several different wig files in a unique result file
multiread_CSEMDispatch: Multiread scoring CSEM dispatch
multiread_RemoveArtifact: Artifact Remover
multiread_UniformDispatch: Multiread scoring uniform dispatch
normAndSubtract: Normalization and subtraction of WIG files
PASHA-package: Pasha package (Preprocessing of Aligned Sequences from HTS...
pileupDouble: Piling vector of double
plotReadsRepartitionAnnotations: Graphical information about reads and annotations repartition
processPipeline: A pipeline to accurately transform aligned reads to genomic...
testFunctional: Functions dedicated to the functional validation of Pasha...
testMultireadFunctional: Functions dedicated to the functional validation of multiread...
wigIO: Read and Write genomic WIG (fixed step) files
WigRepeatAnalyzer: WIG Repeat Analyzer

Functions

.testFunctional Man page
.testFunctionalMultiread Man page
.testFunctionalMultiread_generateResults Man page
.testFunctional_generateResults Man page
AlignedData Man page
AlignedData-class Man page
AnalyzeRepeat Man page
CSEMDispatch Man page
C_binVector Man page
C_elongationEstimation Man page
C_pileupDouble Man page
Pasha Man page
Pasha-package Man page
RemoveArtifact Man page
UniformDispatch Man page
WigRepeatAnalyzer Man page
[,AlignedData,ANY,ANY-method Man page
binVector Man page
checkPairsOK Man page
checkPairsOK,AlignedData-method Man page
cleanNonSimplePairs Man page
cleanNonSimplePairs,AlignedData-method Man page
dropChromosomePattern Man page
dropChromosomePattern,AlignedData-method Man page
dropUndefinedStrand Man page
dropUndefinedStrand,AlignedData-method Man page
elongationEstimation Man page
estimateElongationSize Man page
filterInsertSize Man page
filterInsertSize,AlignedData-method Man page
filterReadSize Man page
filterReadSize,AlignedData-method Man page
flag Man page
flag,AlignedData-method Man page
flag<- Man page
flag<-,AlignedData-method Man page
generatePiled Man page
getArtefactsIndexes Man page
getOrphansIndexes Man page
getOrphansIndexes,AlignedData-method Man page
getStats,AlignedData-method Man page
initialize Man page
isize Man page
isize,AlignedData-method Man page
isize<- Man page
isize<-,AlignedData-method Man page
length Man page
length,AlignedData-method Man page
mapq Man page
mapq,AlignedData-method Man page
mapq<- Man page
mapq<-,AlignedData-method Man page
mergeWigs Man page
mrnm Man page
mrnm,AlignedData-method Man page
mrnm<- Man page
mrnm<-,AlignedData-method Man page
multiread_CSEMDispatch Man page
multiread_RemoveArtifact Man page
multiread_UniformDispatch Man page
normAndSubtractWIG Man page
normalizeChrNames Man page
normalizeChrNames,AlignedData-method Man page
notAligned Man page
notAligned,AlignedData-method Man page
notAligned<- Man page
notAligned<-,AlignedData-method Man page
pairedEnds Man page
pairedEnds,AlignedData-method Man page
pairedEnds<- Man page
pairedEnds<-,AlignedData-method Man page
pileupDouble Man page
plotReadsRepartitionAnnotations Man page
position Man page
position,AlignedData-method Man page
position<- Man page
position<-,AlignedData-method Man page
processPipeline Man page
qwidth Man page
qwidth,AlignedData-method Man page
qwidth<- Man page
qwidth<-,AlignedData-method Man page
readAlignedData Man page
readID Man page
readID,AlignedData-method Man page
readID<- Man page
readID<-,AlignedData-method Man page
readMultipleAlignedData Man page
readWIG Man page
seqnames Man page
seqnames,AlignedData-method Man page
seqnames<- Man page
seqnames<-,AlignedData-method Man page
sortByPairs Man page
sortByPairs,AlignedData-method Man page
strand Man page
strand,AlignedData-method Man page
strand<- Man page
strand<-,AlignedData-method Man page
weight Man page
weight,AlignedData-method Man page
weight<- Man page
weight<-,AlignedData-method Man page
writeWIG Man page

Files

Pasha
Pasha/inst
Pasha/inst/resources
Pasha/inst/resources/mm9.ref
Pasha/inst/resources/ce10.ref
Pasha/inst/resources/dm3.ref
Pasha/inst/resources/hg18.ref
Pasha/inst/resources/hg19.ref
Pasha/inst/resources/sacCer3.ref
Pasha/inst/extdata
Pasha/inst/extdata/embedDataTest.sam
Pasha/inst/extdata/resultsFromFunctionalTestsWIG.tar.gz
Pasha/inst/extdata/resultsFromMultireadFunctionalTests.tar.gz
Pasha/inst/extdata/embededDataTest_MultiSignal.txt
Pasha/inst/extdata/mm9_RepeatMasker_2000l.txt
Pasha/inst/extdata/embedDataTest.bam
Pasha/inst/extdata/resultTests.pdf
Pasha/inst/extdata/embededDataTest_MultiSignal.bow
Pasha/inst/extdata/embedDataTest.bam.bai
Pasha/inst/doc
Pasha/inst/doc/Pasha.Rnw
Pasha/inst/doc/Pasha.R
Pasha/inst/doc/Pasha.pdf
Pasha/tests
Pasha/tests/test_Pasha.Rout.save
Pasha/tests/test_Pasha.R
Pasha/src
Pasha/src/WigRepeatAnalyzerMain.cpp
Pasha/src/AlignedTag.h
Pasha/src/regex.h
Pasha/src/RepeatLocus.cpp
Pasha/src/WigRepeatAnalyzer.cpp
Pasha/src/MultireadCSEMDispatcherMain.cpp
Pasha/src/MultireadDispatcher.h
Pasha/src/WigLocus.h
Pasha/src/MultireadArtifactRemover.cpp
Pasha/src/RepeatLocus.h
Pasha/src/R_init_Pasha.c
Pasha/src/pileupDouble.c
Pasha/src/MultireadCSEMBcTree.h
Pasha/src/binVector.c
Pasha/src/MultireadDispatcherMain.cpp
Pasha/src/WigLocus.cpp
Pasha/src/MultireadCSEMPosPair.h
Pasha/src/MultireadArtifactRemoverMain.cpp
Pasha/src/MultireadDispatcher.cpp
Pasha/src/WigRepeatAnalyzer.h
Pasha/src/AlignedTag.cpp
Pasha/src/elongationEstimation.c
Pasha/src/MultireadArtifactRemover.h
Pasha/NAMESPACE
Pasha/NEWS
Pasha/R
Pasha/R/multiread_RemoveArtifact.R
Pasha/R/binVector.R
Pasha/R/plotReadsRepartitionAnnotations.R
Pasha/R/test_functional.R
Pasha/R/elongationEstimation.R
Pasha/R/test_functional_multiread.R
Pasha/R/multiread_UniformDispatch.R
Pasha/R/WigRepeatAnalyzer.R
Pasha/R/pipelineChipSeq.R
Pasha/R/multiread_CSEMDispatch.R
Pasha/R/Class_AlignedData.R
Pasha/R/pileupDouble.R
Pasha/R/readAlignedBAM_minimalSEQ.R
Pasha/R/normAndSubtract.R
Pasha/R/mergeWigs.R
Pasha/R/wigIO.R
Pasha/vignettes
Pasha/vignettes/Pasha.Rnw
Pasha/MD5
Pasha/build
Pasha/build/vignette.rds
Pasha/DESCRIPTION
Pasha/man
Pasha/man/binVector.Rd
Pasha/man/testMultireadFunctional.Rd
Pasha/man/normAndSubtract.Rd
Pasha/man/mergeWigs.Rd
Pasha/man/multiread_RemoveArtifact.Rd
Pasha/man/multiread_UniformDispatch.Rd
Pasha/man/elongationEstimation.Rd
Pasha/man/estimateElongationSize.Rd
Pasha/man/getArtefactsIndexes.Rd
Pasha/man/pileupDouble.Rd
Pasha/man/PASHA-package.Rd
Pasha/man/wigIO.Rd
Pasha/man/processPipeline.Rd
Pasha/man/WigRepeatAnalyzer.Rd
Pasha/man/plotReadsRepartitionAnnotations.Rd
Pasha/man/generatePiled.Rd
Pasha/man/AlignedData-class.Rd
Pasha/man/testFunctional.Rd
Pasha/man/multiread_CSEMDispatch.Rd
Pasha documentation built on Jan. 15, 2017, 6:21 p.m.