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 <email@example.com>|
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