Differential Methylated Region Analysis Tool
dmr_analysis Documentation
dmr_analysis is a software tool for differentially Methylated Regions analysis to rank significant DMRs.
Contents:
Contents of the package:
The package folder will contain the following:
final_demo: Contains function scripts.dmr_analysis: Contains python source code of the pipeline.readme.txt: Instructions about the usage of the package.requirements.txt: List of requirements. Can be used for automatic installation from miniconda or pip.setup.py: Setup file for the package.final_demo_data: Contains data in and out for the secondary functions.
Pipeline Tasks:
The pipeline consists of the following tasks. To run a task, type dmr_analysis task args. To see what are the options for each task of the pipeline, please run: dmr_analysis -h
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 regression 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 chromatin segments generated from 6 human cell lines.dmr_cal2genome_percent: Calculate the percentage of DMRs intersected with predefined genomic regions such as TSS, TES, 5dist et al.dmr_cal2chromSegment_percent: Calculate the percentage of DMRs intersected with chromatin segments generated from 6 human cells.dmr_percent2plot: Plot the 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: Clean the reference file and create 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/