README

# dmr_analysis

DMR-Analysis: A Differentially Methylated Region Analysis Tool

usage: dmr_analysis task args

## Tasks available for using: <ul>

<li>
<code>dmr_analysis_block</code> - Predict Differentially Methylated Region (DMR) from genome-wide methylation regions such as by using WGBS or other similar techniques </li>

<li>
<code>dmr_combine_multChrs4rank</code> - Combine predicted DMRs/MRs from multiple chromosomes then rank the DMRs by using logistic regresssion model

</li>

<li>
<code>dmr_selected4plot</code> - Plot figure and export raw/smoothed methylation data for selected DMR or MR

</li> <li>

<code>dmr_map2genome</code> - Map all DMR/MRs to reference genome

</li> <li>

<code>dmr_map2chromSegment</code> - Map all DMR/MRs to chromation segments generated from 6 human cell lines

</li> <li>

<code>dmr_cal2genome_percent</code> - Calculate percentage of DMRs intersected with predefined genomic regions such as TSS, TES, 5dist et al.

</li> <li>

<code>dmr_cal2chromSegment_percent</code> - Calculate percentage of DMRs intersected with chromatin segments generated from 6 human celles

</li> <li>

<code>dmr_percent2plot</code> - Plot percentage of DMRs in predefined genomic or chromatin segment regions

</li> <li>

<code>dmr_combine2geneAnnot</code> - Combine annotations from both predefined genomic regions and chromatin segments (This function is slow and requests both genome and chromatin segment results available)

</li> <li>

<code>dmr_exportData</code> - Plot and export data for DMRs/MRs located in specific regions (e.g., DMRs/MRs intersected with mutation block or enhancer regions)

</li>

<li><code>dmr_gene_annotation</code>:

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/

</li>

</ul>

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 go to look inside the code here: [https://github.com/dmr-analysis/dmr_analysis](https://github.com/dmr-analysis/dmr_analysis)