Function reference • CLIPflexR

CTK CTK wrapper functions.
`install_ctk()`	Install ctk pipeline
`ctk_cits()`	Wrapper function for ctk's CITS
`ctk_getMutationType()`	Wrapper function for ctk's getMutationType
`ctk_fastqFilter()`	Wrapper function for ctk's fastq_filter
`ctk_fastq2collapse()`	Wrapper function for ctk's fastq2collapse
`ctk_stripBarcode()`	Wrapper function for ctk's stripBarcode
`ctk_parseAlignment()`	Wrapper function for ctk's parseAlignment
`ctk_tag2collapse()`	Wrapper function for ctk's tag2collapse
`ctk_bed2rgb()`	Wrapper function for ctk's bed2rgb
`ctk_tag2profile()`	Wrapper function for ctk's ctk_tag2profile
`ctk_cims()`	Wrapper function for ctk's CIMS
`ctk_joinWrapper()`	Wrapper function for galaxy's joinWrapper
`ctk_tag2peak()`	Wrapper function for ctk's bed2rgb
Alignment Alignment functions.
`bowtie2_index()`	Make index for Rbowtie2
`bowtie_align()`	Alignment using Rbowtie2
`CLIP_buildIDX()`	Build index for reference genome
`CLIP_align()`	Align to Genome
Homer Homer wrapper functions.
`homer_peaks()`	Wrapper function for Homer's makeTagDirectory and findPeaks
FastX FastX toolkit wrapper functions.
`fastx_qtoa()`	Wrapper function for fastq_to_fasta
`fastx_quality_stats()`	Wrapper function for fastx_quality_stats
`fastx_collapser()`	Wrapper function for fastx_collapser
`fastx_barcode_splitter()`	Wrapper function for fastx_barcode_splitter
`fastq_quality_filter()`	Wrapper function for fastq_quality_filter
`fastx_clipper()`	Wrapper function for fastx_clipper
`fastq_quality_trimmer()`	Wrapper function for fastq_quality_trimmer
`fastx_trimmer()`	Wrapper function for fastx_trimmer
Compress/Decompress Compress/Decompress utility functions.
`decompress()`	Wrapper function for gunzip, bunzip
`compress()`	Wrapper function for gzip, bzip
`bzip2()`	Wrapper function for bzip2
R utility functions Useful R functions for CLIP processing/analyses.
`bamtobed()`	Convert Bam to Bed
`extract_unmapped()`	Extracts unmapped reads from BAM and writes them to a FASTA file
`countFromBed()`	Count from beds to make count matrix
`CLIP_bw2()`	Build bigwigs
`annotatePeaksWithPatterns()`	Search for small RNA targets, or any pattern, in peaks
`fetchSequencesForCLIP()`	Retrieve sequences from under peaks/regions
`revmap_process()`	Process reads to remove linker artifacts or filter by length
`revmap_count()`	Reverse map small RNAs to processed or unprocessed reads
`ranges_count()`	Map unprocessed or processed reads to genome and count small RNAs by location
`chimera_Process()`	Chimera process CLIP data

Reference

CTK

Alignment

Homer

FastX

Compress/Decompress

R utility functions