zekaihuang-pku / richteromicscode

RichterOmicsCode

Main dataset generation, integration and score computation code for the Richter Syndrome multi-omics project.

1. methylome datasets (microarrays): QC, checks, filtering, normalization, batch effect removal, explorations, statistics, DMRs, ... and more
2. transcriptome datasets (NGS): QC, splice-aware mapping, transcripts reconstruction, variant calling from expressed coding regions, variant annotation, filtering and normalization
3. methylome <-> transcriptome data integration and extraction of correlated regions within regulatory features
4. linear predictor score (LPS statistics) computation from methylation data, along with 4863-CpG signature
5. linear classifier score (LCS statistics) computation from expression datasets, along with 215-gene signature