Pasha: Preprocessing of Aligned Sequences from HTS Analyses

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).

Author
Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Benoukraf, Pierre Cauchy, Charlene Innocenti, Pierre Ferrier, Jean-Christophe Andrau
Date of publication
2016-03-18 16:23:47
Maintainer
Romain Fenouil <romain.fenouil@mssm.edu>
License
GPL-3
Version
0.99.21

View on CRAN

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

Files in this package

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