inst/scripts/crispr_benchmark/README.md

In cbg-ethz/dce: Pathway Enrichment Based on Differential Causal Effects

CRISPR

Benchmark dce method on CRISPR data. Here, we try to recover de-regulated pathway intreractions caused by a gene knock-out.

• Data source:
  • Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315571/
  • Accession: GSE90546

Data layout

Exemplary layout of data folder:

$ tree data/
data/
├── epistasis
│   ├── Counts_ATF6,EIF2AK3_1.csv
│   ├── Counts_ATF6,EIF2AK3_2.csv
│   ├── Counts_ATF6,EIF2AK3_3.csv
│   ├── Counts_ATF6_1.csv
│   ├── Counts_ATF6_2.csv
│   ├── Counts_ATF6_3.csv
│   ├── Counts_Ctrl_1.csv
│   ├── Counts_Ctrl_2.csv
│   ├── Counts_Ctrl_3.csv
│   ├── Counts_EIF2AK3_1.csv
│   ├── Counts_EIF2AK3_2.csv
│   ├── Counts_EIF2AK3_3.csv
│   ├── Counts_ERN1_1.csv
│   ├── Counts_ERN1_2.csv
│   └── Counts_ERN1_3.csv
└── main
    ├── Counts_Ctrl_1.csv
    ├── Counts_Ctrl_2.csv
    ├── Counts_Ctrl_3.csv
    ├── Counts_EIF2S1_1.csv
    ├── Counts_EIF2S1_2.csv
    └── Counts_EIF2S1_3.csv

cbg-ethz/dce documentation built on Oct. 29, 2022, 8:14 a.m.