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.

AuthorAnita Lerch, Dimos Gaiditzis and Michael Stadler
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 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

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

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