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