An integrated data analysis pipeline by considering both Differential Methylation Region (DMR) and Differential Expression Gene (DEG) in SNP analysis. This package depends on some functions from the bpb3 package!
positional arguments: - task: Pipeline task to run
optional arguments: - -h, --help: Show this help message and exit Usage: dds_analysis <task> [<args>]
- bpb3summary2bed_format: Convert bpb3 block summary file to a bed format file
- map_block2genome: Map mutation block to genomic regions
- map_block2chromSegment: Map mutation block to chromatin Segment regions
- map_block2dmr: Map mutation block to differential methylated regions
- find_geneExp4block: Find differential expressed genes for mutation blocks
- find_block_patieintID: Find patient ID for mutation blocks
- combine_dmr_deg2block: Combine DMR, DEG, and mutation block information together
- filter_blocks: Filter mutation blocks by using DMR or/and DEG condition
- collect_gene_names4blocks: Collect unique gene names for mutation blocks with DMR and/or DEG
- check_block_gene_inTAD: Check whether block and gene are in the same TAD or TAD boundary
- dds_geneRanking: Select top-ranked genes from final prediction
- go_pathway_analysis4out_blocks_gene: GO pathway analysis of genes
- find_enhancer_target_genes: Find enhancer and its target genes overlapping with mutation blocks that associated with selected gene
- chromSegment_test4blocks: Enrichment test of mutation blocks or methylation regions that associated with genes in 7 chromatin segmentations of the human genome
- dTarget_methy_vs_express: Predict long-distance target gene for a specific region (e.g., mutation block) based on coupling of methylation and gene expression across samples
- plot_mr_vs_exp: Plot DMR/MR methylation level and Gene expression for a pair of DMR and its target gene
- plot_tss_enhancer_mrs: Plot the average methylation level of predicted DMRs at TSS and enhancer regions by the target genes predicted from dTarget_methy_vs_express
- filterDEG4bpb3: Filter Differential Expressed Genes (DEG) by rratio based on the exported file from bpb3 differential_expression then export it with group mean and rratio
- preprocess: This module first finds DEG in TSS, 5dist regions then preprocesses data for dds_analysis.
A detailed documentation of the tool can be found here: https://dds-analysis.readthedocs.io/en/latest/index.html