QuasR: Quantify and Annotate Short Reads in R

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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.

Author
Anita Lerch, Dimos Gaiditzis and Michael Stadler
Date of publication
None
Maintainer
Michael Stadler <michael.stadler@fmi.ch>
License
GPL-2
Version
1.14.0

View on Bioconductor

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

Files in this package

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