Man pages for kathrynrozengagnon/CLIPflexR
CLIP tools and wrappers in R
| annotatePeaksWithPatterns | Search for small RNA targets, or any pattern, in peaks |
| bamtobed | Convert Bam to Bed |
| bowtie2_index | Make index for Rbowtie2 |
| bowtie_align | Alignment using Rbowtie2 |
| bzip2 | Wrapper function for bzip2 |
| chimera_process | Chimera process CLIP data |
| ClIP_align | Align to Genome |
| CLIP_buildIDX | Build index for reference genome |
| ClIP_bw2 | Build bigwigs |
| compress | Wrapper function for gzip, bzip |
| countFromBed | Count from beds to make count matrix |
| ctk_bed2rgb | Wrapper function for ctk's bed2rgb |
| ctk_cims | Wrapper function for ctk's CIMS |
| ctk_cits | Wrapper function for ctk's CITS |
| ctk_fastq2collapse | Wrapper function for ctk's fastq2collapse |
| ctk_fastqFilter | Wrapper function for ctk's fastq_filter |
| ctk_getMutationType | Wrapper function for ctk's getMutationType |
| ctk_joinWrapper | Wrapper function for galaxy's joinWrapper |
| ctk_parseAlignment | Wrapper function for ctk's parseAlignment |
| ctk_stripBarcode | Wrapper function for ctk's stripBarcode |
| ctk_tag2collapse | Wrapper function for ctk's tag2collapse |
| ctk_tag2peak | Wrapper function for ctk's bed2rgb |
| ctk_tag2profile | Wrapper function for ctk's ctk_tag2profile |
| decompress | Wrapper function for gunzip, bunzip |
| extract_unmapped | Extracts unmapped reads from BAM and writes them to a FASTA... |
| fastq_quality_filter | Wrapper function for fastq_quality_filter |
| fastq_quality_trimmer | Wrapper function for fastq_quality_trimmer |
| fastq_to_fasta | Wrapper function for fastq_to_fasta |
| fastx_barcode_splitter | Wrapper function for fastx_barcode_splitter |
| fastx_clipper | Wrapper function for fastx_clipper |
| fastx_collapser | Wrapper function for fastx_collapser |
| fastx_quality_stats | Wrapper function for fastx_quality_stats |
| fastx_trimmer | Wrapper function for fastx_trimmer |
| fetchSequencesForClIP | Retrieve sequences from under peaks/regions |
| homer_peaks | Wrapper function for Homer's makeTagDirectory and findPeaks |
| install_ctk | Install ctk pipeline |
| Ranges_count | Map unprocessed or processed reads to genome and count small... |
| revmap_count | Reverse map small RNAs to processed or unprocessed reads |
| revmap_process | Process reads to remove linker artifacts or filter by length |
