Pipelines and scripts to reproduce the analysis in Fischer et al., Cell Reports (2024) PMID: 39084219 https://doi.org/10.1016/j.celrep.2024.114498
Original code release: DOI 10.5281/zenodo.12516010
The repository is structured based on data packages that were analysed partially dependent from each other. This includes the following analyses in the order listed:
- Scripts to analyse mutation screening data (Mutations folder)
- Scripts and input csv files to analyse and visualize HSPC culture expansion rates, genome editing rates and colony forming untit (CFU) results (HSPC_cultures folder)
- Pipelines for mapping ChIP/ATAC/RNA-seq and routine scripts used for several downstream analyses (Pipelines folder)
- Scripts to analyse and visualize RNA-seq results after mapping (RNAseq folder)
- Scripts to analyse and visualize single cell RNA-seq data (scRNAseq folder)
- Scripts and input csv files to analyse and visualize actin-normalized western blots (WB_actin_norm folder)
- Scripts to analyse and visualize ATAC-seq results after mapping (ATACseq folder)
- Scripts to analyse and visualize ChIP-seq results after mapping, contains subdirectories by antibody (ChIPseq folder)
- Scripts for mapping, analyzing and visualizing Hi-C data, inlcluding matrix processing via the FAN-C suite (HiC folder)
- Scripts to integrate and correlate transcriptomic results with epigentic assays (ATAC/ChIP/HiC)(Epigenetic_GEX_correlations folder)