Man pages for mireia-bioinfo/pipelineNGS
Methods for Epigenetic Data Processing
| alignmentBowtie2 | Alignment with Bowtie 2 |
| bamToBigWig | Conversion from BAM to visualization formats |
| callPeak | Peak calling with MACS2 |
| dot-getBDGforSEACR | Obtain bedgraph files for SEACR input |
| fastqc | Quality Control with FastQC |
| filtOutBAM | Filter out reads from BAM file |
| getNameFromPath | Get name from path |
| getStats | Get alignment and processing stats from BAM files |
| mergeBAMs | Merge BAM files |
| offsetATAC | Offset correction for ATAC-seq data |
| offsetATACSE | Offset correction for SE ATAC-seq data |
| paramdata | Data parameters for different experiments |
| peakCallingSEACR | CUT&TAG peak calling with SEACR |
| pipelineNGS | Pipeline for Next-Generation Sequencing Experiments |
| plotAlignment | Plot alignment statistics |
| processCUTTAG | Automated processing of CUT&TAG samples |
| process_epigenome | Automated processing of ChIP-seq and ATAC-seq samples |
| tableFromIdxstats | Table form idxstats |
