Files in kathrynrozengagnon/CLIPflexR

CLIP tools and wrappers in R

.Rbuildignore

.github/.gitignore

.github/workflows/selfTest.yml

.gitignore

DESCRIPTION

NAMESPACE

R/Functions.R R/install_ctk.R R/wrapperFunctions_ctk.R R/wrapperFunctions_fastxtoolkit.R R/wrapperFunctions_homer.R R/zzz.R README.Rmd README.md

_pkgdown.yml

docs/404.html

docs/README.Rmd.html

docs/articles/Processing_to_matrix.html

docs/articles/StandardandBrdU_Processing_CTK.html

docs/articles/chimera_vignette.html

docs/articles/index.html

docs/articles/installCliPR.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/CLIP_buildIDX.html

docs/reference/ClIP_align.html

docs/reference/ClIP_bw2.html

docs/reference/Ranges_count.html

docs/reference/annotatePeaksWithPatterns.html

docs/reference/bamtobed.html

docs/reference/bowtie2_index.html

docs/reference/bowtie_align.html

docs/reference/bzip2.html

docs/reference/chimera_process.html

docs/reference/compress.html

docs/reference/countFromBed.html

docs/reference/ctk_bed2rgb.html

docs/reference/ctk_cims.html

docs/reference/ctk_cits.html

docs/reference/ctk_fastq2collapse.html

docs/reference/ctk_fastqFilter.html

docs/reference/ctk_getMutationType.html

docs/reference/ctk_joinWrapper.html

docs/reference/ctk_parseAlignment.html

docs/reference/ctk_stripBarcode.html

docs/reference/ctk_tag2collapse.html

docs/reference/ctk_tag2peak.html

docs/reference/ctk_tag2profile.html

docs/reference/decompress.html

docs/reference/extract_unmapped.html

docs/reference/fastq_quality_filter.html

docs/reference/fastq_quality_trimmer.html

docs/reference/fastq_to_fasta.html

docs/reference/fastx_barcode_splitter.html

docs/reference/fastx_clipper.html

docs/reference/fastx_collapser.html

docs/reference/fastx_quality_stats.html

docs/reference/fastx_trimmer.html

docs/reference/fetchSequencesForClIP.html

docs/reference/hello.html

docs/reference/homer_peaks.html

docs/reference/index.html

docs/reference/install_ctk.html

docs/reference/readinpeaks.html

docs/reference/revmap_count.html

docs/reference/revmap_process.html

inst/.gitignore

inst/extdata/BrdU.Fox.pool.tag.uniq.mutation.small.txt

inst/extdata/BrdU.Fox.pool.tag.uniq.rgb.small.bed

inst/extdata/Fox.pool.tag.uniq.rgb.small.bed

inst/extdata/Fox3_Std_small.fq.gz

inst/extdata/R-CMD-check.yaml

inst/extdata/SRR1742056.fastq.gz

inst/extdata/check-bioc.yml

inst/extdata/getData.R

inst/extdata/hg19Small.fa

inst/extdata/hsa_mature.fa

inst/extdata/joinWrapper.py

man/CLIP_buildIDX.Rd man/ClIP_align.Rd man/ClIP_bw2.Rd man/Ranges_count.Rd man/annotatePeaksWithPatterns.Rd man/bamtobed.Rd man/bowtie2_index.Rd man/bowtie_align.Rd man/bzip2.Rd man/chimera_process.Rd man/compress.Rd man/countFromBed.Rd man/ctk_bed2rgb.Rd man/ctk_cims.Rd man/ctk_cits.Rd man/ctk_fastq2collapse.Rd man/ctk_fastqFilter.Rd man/ctk_getMutationType.Rd man/ctk_joinWrapper.Rd man/ctk_parseAlignment.Rd man/ctk_stripBarcode.Rd man/ctk_tag2collapse.Rd man/ctk_tag2peak.Rd man/ctk_tag2profile.Rd man/decompress.Rd man/extract_unmapped.Rd man/fastq_quality_filter.Rd man/fastq_quality_trimmer.Rd man/fastq_to_fasta.Rd man/fastx_barcode_splitter.Rd man/fastx_clipper.Rd man/fastx_collapser.Rd man/fastx_quality_stats.Rd man/fastx_trimmer.Rd man/fetchSequencesForClIP.Rd man/homer_peaks.Rd man/install_ctk.Rd man/revmap_count.Rd man/revmap_process.Rd

vignettes/.gitignore

vignettes/Processing_to_matrix.Rmd

vignettes/SRR1107535_Test.fastq

vignettes/StandardandBrdU_Processing_CTK.Rmd

vignettes/annotate-1.png

vignettes/chimera.png

vignettes/chimera_vignette.Rmd vignettes/installCliPR.Rmd

vignettes/miRNA_counts.png

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.