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DMRichR v1.3.0
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@ben-laufer ben-laufer released this 26 Apr 21:02
· 61 commits to master since this release
v1.3.0
4af9ef7

Key updates:

  1. Expanded supported genomes to: hg38, hg19, mm10, mm9, rheMac10, rheMac8, rn6, danRer11, galGal6, bosTau9, panTro6, dm6, canFam3, susScr11, and TAIR9.

  2. Resource optimization: DM.R should use between 10-20 cores and 64-256 GB of RAM.

  3. Optimized block calling parameters.

  4. densityPlot() is now for single CpGs instead of 20 KB windows, which makes it more similar to array output.

  5. Added a beta feature for cell composition estimation in human whole blood using two separate methods: Houseman and methylCC. CCstats() and CCplot() are novel functions for downstream statistical analysis and visualization. The feature can be utilized by adding --cellComposition = TRUE to the DM.R call.

  6. Tidying of the annotation pipeline to add gene symbols, percent difference, and directionality to regions of interest, where annotateRegions() was developed from previous helper functions and code in DM.R

  7. Added annotations for blocks, where DMReport() now supports blocks and DM.R generates an HTML block report

  8. Gene ontology analyses are now performed for all DMRs, hypermethylated DMRs, and hypomethylated DMRs.

  9. Added arrayLift() to liftOver Illumina array (EPIC, 450K, and 27K) CpG IDs to hg38 coordinates.

  10. Added LOLA enrichment testing and heatmaps for the ChromHMM 15-state model and Roadmap Epigenomics core histone modifications for hg38. Currently, this will only run on the UC Davis Cluster due to needing large external databases; however, an advanced user can download the databases and make minor modifications to the functions [chromHMM(), chromHMM_heatmap(), roadmap(), and roadmap_heatmap()] to refer to their local copy.

  11. Tidying, minor bug fixes, and documentation updates.

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