https://github.com/gagneurlab/leukemia_outlier
https://github.com/gagneurlab/leukemia_outlier
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/gagneurlab/leukemia_outlier
- Owner: gagneurlab
- Created: 2023-09-14T08:28:57.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-06-10T14:05:04.000Z (12 months ago)
- Last Synced: 2025-02-03T13:26:56.765Z (4 months ago)
- Language: R
- Size: 9.88 MB
- Stars: 2
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: readme.md
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README
# Leukemia outlier
Aberrant genome and transcriptome analysis of 3,760 hematologic malignancies.
See manuscript at https://doi.org/10.1186/s13073-024-01331-6
A website for data exploration and visualization is available at https://leukemia-outlier.cmm.cit.tum.de/
## OUTRIDER
OUTRIDER was run using branch `outrider2` (https://github.com/gagneurlab/OUTRIDER/tree/outrider2) and DROP v 1.1.0 (https://github.com/gagneurlab/drop/releases/tag/1.1.0)
## FRASER
FRASER was run using v 1.99.0 (https://github.com/c-mertes/FRASER/releases/tag/1.99.0) and DROP v 1.2.3 (https://github.com/gagneurlab/drop/releases/tag/1.2.3)
## AbSplice
AbSplice was run using v 1.0.0 (https://github.com/gagneurlab/absplice)
## intOGen
intOGen was run on version commit 437a047 (https://bitbucket.org/intogen/intogen-plus/src/437a0473b3ccb187415b6b2fc68c5b7fbe15ae3e/)
### Run intOGen
1. Move to intOGen folder
`cd intogen-plus`
2. Download file
`wget https://bitbucket.org/intogen/intogen-plus/src/437a0473b3ccb187415b6b2fc68c5b7fbe15ae3e/build/containers/dndscv/dndscv.tar.gz`
3. Move file
`mv dndscv.tar.gz build/containers/dndscv/`
4. Run intOGen as `README.md`
## Driver gene prediction
Pipeline to identify leukemia driver gene.
### Run driver gene prediction
See `driver_gene_prediction/readme.md`