Files in fmicompbio/QuasR
Quantify and Annotate Short Reads in R

.BBSoptions
.Rbuildignore
.travis.yml
DESCRIPTION
NAMESPACE
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
appveyor.yml
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/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
src/Makevars
src/R_init_QuasR.cpp
src/bam.c
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.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 Nov. 8, 2019, 9:42 a.m.