This is a repository for IDR variant catalogue of the paper
Mensah & Niskanen et al.
"Aberrant phase separation and nucleolar dysfunction can underlie rare genetic diseases 2023"
Author: Alexandre P Magalhaes
R libraries required:
ensembldb rtracklayer AnnotationHub biomaRt
Python libraries required:
pandas numpy matplotlib pickle metapredict Biopython localcider pandarallel
Python vep enviroment.yml is avalable as VEP conflicts with the main enviroment
Databases Used
- GENCODE GRCh38.p13 Release 41 https://www.gencodegenes.org/human/
- MobiDB 4.1.0 https://mobidb.bio.unipd.it/
- Ensembldb v104 https://bioconductor.org/packages/release/bioc/html/ensembldb.html
- Clinvar 1.64 https://www.ncbi.nlm.nih.gov/clinvar/
- COSMIC v95 https://cancer.sanger.ac.uk/cosmic
- dbDNP from May 26, 2020 https://www.ncbi.nlm.nih.gov/snp/
- 1000 genomes from 2021-11-20 https://www.internationalgenome.org/data
and Database tools version used
- Ensembldb v2.22.0
- VEP v104
Just follow the numbered folders and scripts
Any questions: magalhae@molgen.mpg.de