Files in fmicompbio/QuasR

Quantify and Annotate Short Reads in R

.Rbuildignore

.github/workflows/R-CMD-check.yaml

.github/workflows/run_rchk.yaml

DESCRIPTION

NAMESPACE

R/QuasR-package.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/utilities.R README.md

codecov.yml

inst/AlignerIndexPkg-template/DESCRIPTION

inst/AlignerIndexPkg-template/NAMESPACE

inst/AlignerIndexPkg-template/R/.gitignore

inst/AlignerIndexPkg-template/inst/dummy.txt

inst/AlignerIndexPkg-template/man/package.Rd

inst/CITATION

inst/NEWS

inst/extdata/BSgenome.HSapiens.QuasR.hg19sub_0.1.0.tar.gz

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

man/QuasR-package.Rd man/alignmentStats.Rd man/dot-get_alnstats_for_bam.Rd man/preprocessReads.Rd man/qAlign.Rd man/qCount.Rd man/qExportWig.Rd man/qMeth.Rd man/qProfile.Rd man/qProject-class.Rd man/qProjectUpdate.Rd man/qQCReport.Rd man/worker_message.Rd

src/Makevars

src/R_init_QuasR.cpp

src/bam_cat.c

src/bam_plbuf.c

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/filter_hisat2.c

src/filter_hisat2.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/sam_opts.c

src/sam_utils.c

src/split_sam_chr.c

src/split_sam_chr.h

src/utilities.c

src/utilities.h

tests/testthat.R tests/testthat/helper_create-synthetic-qProject.R tests/testthat/setup_test-environment.R tests/testthat/teardown_test-environment.R tests/testthat/test_createAlignments-functions.R tests/testthat/test_preprocessReads.R tests/testthat/test_qAlign.R tests/testthat/test_qCount.R tests/testthat/test_qExportWig.R tests/testthat/test_qMeth.R tests/testthat/test_qProfile.R tests/testthat/test_qProject.R tests/testthat/test_qQCReport.R tests/testthat/test_src.R tests/testthat/test_utilites.R vignettes/QuasR-logo.pdf

vignettes/QuasR-logo.png

vignettes/QuasR-refs.bib

vignettes/QuasR-scheme.png

vignettes/QuasR.Rmd

fmicompbio/QuasR documentation built on March 19, 2024, 5:33 a.m.