DMR-Analysis: A Differentially Methylated Region Analysis Tool
usage: dmr_analysis task args
-
dmr_analysis_block- Predict Differentially Methylated Region (DMR) from genome-wide methylation regions such as by using WGBS or other similar techniques -
dmr_combine_multChrs4rank- Combine predicted DMRs/MRs from multiple chromosomes then rank the DMRs by using logistic regresssion model -
dmr_selected4plot- Plot figure and export raw/smoothed methylation data for selected DMR or MR -
dmr_map2genome- Map all DMR/MRs to reference genome -
dmr_map2chromSegment- Map all DMR/MRs to chromation segments generated from 6 human cell lines -
dmr_cal2genome_percent- Calculate percentage of DMRs intersected with predefined genomic regions such as TSS, TES, 5dist et al. -
dmr_cal2chromSegment_percent- Calculate percentage of DMRs intersected with chromatin segments generated from 6 human celles -
dmr_percent2plot- Plot percentage of DMRs in predefined genomic or chromatin segment regions -
dmr_combine2geneAnnot- Combine annotations from both predefined genomic regions and chromatin segments (This function is slow and requests both genome and chromatin segment results available) -
dmr_exportData- Plot and export data for DMRs/MRs located in specific regions (e.g., DMRs/MRs intersected with mutation block or enhancer regions) dmr_gene_annotation: - Cleans reference file and creates genomic region files (TSS, geneBody, TES, 5dist and intergenic) from the reference. This module is reimplemented here from hmst-seq-analyzer tool https://hmst-seq.github.io/hmst/
DMR-Analysis: A Differentially Methylated Region Analysis Tool
positional arguments: task Pipeline task to run
optional arguments: -h, --help show this help message and exit
Having trouble with package? Contact us @ junbai.wang@medisin.uio.no and we will be glad to help you. You can read the complete documentation here: https://dmr-analysis.readthedocs.io/en/latest/index.html