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).

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

View on CRAN

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

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