QuasR: Quantify and Annotate Short Reads in R
Version 1.16.0

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.

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AuthorAnita Lerch, Dimos Gaiditzis and Michael Stadler
Bioconductor views Alignment ChIPSeq Coverage Genetics MethylSeq Preprocessing QualityControl RNASeq Sequencing
Date of publicationNone
MaintainerMichael Stadler <michael.stadler@fmi.ch>
LicenseGPL-2
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("QuasR")

Man pages

alignmentStats: Get statistics on alignments
preprocessReads: Preprocess Short Reads
qAlign: Align reads
qCount: Quantify alignments
qExportWig: QuasR wig file export
qMeth: Quantify DNA methylation
qProfile: Quantify alignments by relative position
qProject-class: qProject objects
qQCReport: QuasR Quality Control Report
QuasR-package: Quantify and Annotate Short Reads in R

Functions

BSgenomeSeqToFasta Source code
QuasR Man page
QuasR-package Man page
[,qProject,ANY,missing,missing-method Man page
addNumericToID Source code
align_Rbowtie Source code
align_RbowtieCtoT_dir Source code
align_RbowtieCtoT_undir Source code
align_RbowtieSpliced Source code
alignmentStats Man page Source code
alignments Man page
alignments,qProject-method Man page
as.data.frame,qProject-method Man page
auxiliaries Man page
auxiliaries,qProject-method Man page
bamInfoOnlyBaseName Source code
buildIndex Source code
buildIndexPackage Source code
buildIndexSNP Source code
buildIndex_Rbowtie Source code
buildIndex_RbowtieCs Source code
buildIndex_RbowtieCtoT Source code
calcMmInformation Source code
calcQaInformation Source code
class:qProject Man page
compressFile Source code
compressedFileFormat Source code
concatenateFiles Source code
consolidateFileExtensions Source code
countAlignments Source code
countAlignmentsSubregionsC Source code
countJunctionsOneBamfile Source code
createAuxAlignments Source code
createAuxAlignmentsController Source code
createGenomicAlignments Source code
createGenomicAlignmentsController Source code
createQProject Source code
createReferenceSequenceIndices Source code
createSeedList Source code
detectVariantsBamfilesRegionsSingleChromosome Source code
determineSamplesFormat Source code
displayNames Source code
filterLength Source code
filterLowComplexity Source code
freeDiskSpace Source code
genome,qProject-method Man page
getListOfBiocParallelParam Source code
grangesFromGff Source code
length,qProject-method Man page
md5subsum Source code
missingFilesMessage Source code
pathAsAbsoluteRedirected Source code
plotDuplicated Source code
plotErrorsByCycle Source code
plotFragmentDistribution Source code
plotMappings Source code
plotMismatchTypes Source code
plotNuclByCycle Source code
plotQualByCycle Source code
plotUniqueness Source code
preprocessPairedReads Source code
preprocessReads Man page Source code
preprocessSingleReads Source code
profileAlignments Source code
qAlign Man page Source code
qCount Man page Source code
qExportWig Man page Source code
qMeth Man page Source code
qProfile Man page Source code
qProject Man page Man page
qProject-class Man page
qProjectBamInfo Source code
qQCReport Man page Source code
qa_ShortRead Source code
quantifyMethylationBamfilesRegionsSingleChromosome Source code
quantifyMethylationBamfilesRegionsSingleChromosomeAllele Source code
quantifyMethylationBamfilesRegionsSingleChromosomeSingleAlignmen Source code
resolveCacheDir Source code
samToSortedBamCore Source code
samToSortedBamParallel Source code
sampleNames Man page
sampleNames,qProject-method Man page
sampleNames<- Man page
sampleNames<-,qProject-method Man page
show,qProject-method Man page
test Source code
truncPath Source code
truncString Source code
truncStringToPlotWidth Source code
updateObject,qProject-method Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/createAlignments-functions.R
R/createIndex-functions.R
R/preprocessReads.R
R/qAlign.R
R/qCount.R
R/qExportWig.R
R/qMeth.R
R/qProfile.R
R/qProject-class.R
R/qQCReport.R
R/test_QuasR_package.R
R/utilities.R
build
build/vignette.rds
inst
inst/AlignerIndexPkg-template
inst/AlignerIndexPkg-template/DESCRIPTION
inst/AlignerIndexPkg-template/NAMESPACE
inst/AlignerIndexPkg-template/R
inst/AlignerIndexPkg-template/inst
inst/AlignerIndexPkg-template/inst/dummy.txt
inst/AlignerIndexPkg-template/man
inst/AlignerIndexPkg-template/man/package.Rd
inst/CITATION
inst/NEWS
inst/doc
inst/doc/QuasR.R
inst/doc/QuasR.Rnw
inst/doc/QuasR.pdf
inst/extdata
inst/extdata/NC_001422.1.fa
inst/extdata/auxiliaries.txt
inst/extdata/bis_1_1.fa.bz2
inst/extdata/chip_1_1.fq.bz2
inst/extdata/chip_2_1.fq.bz2
inst/extdata/hg19sub.fa
inst/extdata/hg19sub_annotation.gtf
inst/extdata/hg19sub_snp.txt
inst/extdata/mirbaseXX_qsr.gff3
inst/extdata/mirna_1.fa
inst/extdata/phiX_paired_withSecondary.bam
inst/extdata/phiX_paired_withSecondary.bam.bai
inst/extdata/phiX_paired_withSecondary_sampleFile.txt
inst/extdata/rna_1_1.fq.bz2
inst/extdata/rna_1_2.fq.bz2
inst/extdata/rna_2_1.fq.bz2
inst/extdata/rna_2_2.fq.bz2
inst/extdata/samples_bis_single.txt
inst/extdata/samples_chip_single.txt
inst/extdata/samples_mirna.txt
inst/extdata/samples_rna_paired.txt
inst/extdata/samples_rna_single.txt
inst/unitTests
inst/unitTests/help_function.R
inst/unitTests/test_preprocessReads.R
inst/unitTests/test_qAlign.R
inst/unitTests/test_qCount.R
inst/unitTests/test_qExportWig.R
inst/unitTests/test_qMeth.R
inst/unitTests/test_qProfile.R
inst/unitTests/test_qProject.R
inst/unitTests/test_utilities.R
man
man/QuasR-package.Rd
man/alignmentStats.Rd
man/preprocessReads.Rd
man/qAlign.Rd
man/qCount.Rd
man/qExportWig.Rd
man/qMeth.Rd
man/qProfile.Rd
man/qProject-class.Rd
man/qQCReport.Rd
src
src/Makevars
src/Makevars.win
src/R_init_QuasR.cpp
src/cat_bam.c
src/cat_bam.h
src/convert_reads_id_bis_rc.c
src/convert_reads_id_bis_rc.h
src/count_alignments.c
src/count_alignments.h
src/count_alignments_subregions.c
src/count_alignments_subregions.h
src/count_junctions.cpp
src/count_junctions.h
src/export_wig.c
src/export_wig.h
src/extract_unmapped_reads.c
src/extract_unmapped_reads.h
src/idxstats_bam.c
src/idxstats_bam.h
src/merge_reorder_sam.cpp
src/merge_reorder_sam.h
src/nucleotide_alignment_frequencies.c
src/nucleotide_alignment_frequencies.h
src/profile_alignments.c
src/profile_alignments.h
src/quantify_methylation.cpp
src/quantify_methylation.h
src/remove_unmapped_from_sam.c
src/remove_unmapped_from_sam.h
src/split_sam_chr.c
src/split_sam_chr.h
src/utilities.c
src/utilities.h
tests
tests/QuasR_unit_tests.R
vignettes
vignettes/QuasR-logo.pdf
vignettes/QuasR-refs.bib
vignettes/QuasR-scheme.png
vignettes/QuasR.Rnw
QuasR documentation built on May 20, 2017, 9:53 p.m.