QuasR: Quantify and Annotate Short Reads in R

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("QuasR")
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
Version1.14.0

View on Bioconductor

Functions

alignments Man page
alignments,qProject-method Man page
alignmentStats Man page
as.data.frame,qProject-method Man page
auxiliaries Man page
auxiliaries,qProject-method Man page
class:qProject Man page
genome,qProject-method Man page
length,qProject-method Man page
preprocessReads Man page
qAlign Man page
qCount Man page
qExportWig Man page
qMeth Man page
qProfile Man page
qProject Man page
[,qProject,ANY,missing,missing-method Man page
qProject-class Man page
qQCReport Man page
QuasR Man page
QuasR-package Man page
sampleNames Man page
sampleNames<- Man page
sampleNames<-,qProject-method Man page
sampleNames,qProject-method Man page
show,qProject-method Man page
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

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