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
