mdelcorvo / TOSCA
Snakemake workflow for somatic mutation detection without matched normal samples
☆11Updated 2 years ago
Alternatives and similar repositories for TOSCA:
Users that are interested in TOSCA are comparing it to the libraries listed below
- A pipeline for identifying indel derived neoantigens using RNA-Seq data☆30Updated 2 years ago
- MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data☆21Updated last month
- Main repository for Drews et al. (Nature, 2022)☆39Updated last year
- MutSig2CV from Lawrence et al. 2014☆31Updated 4 years ago
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆17Updated 5 years ago
- ☆38Updated 5 years ago
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆34Updated 8 months ago
- Homologous recombination deficiency in TCGA PanCancer Atlas☆27Updated 4 years ago
- SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…☆19Updated last month
- Package for calculation of Homologous Recombination Deficiency☆13Updated 4 years ago
- Comprehensive analysis of small RNA sequencing data☆31Updated 9 months ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆30Updated last year
- Clonality Inference in Multiple Tumor Samples using Phylogeny☆14Updated 9 years ago
- Code accompanying The Evolutionary history of 2,658 cancers☆46Updated 3 years ago
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆43Updated 3 years ago
- Model-based subclonal deconvolution from bulk sequencing.☆33Updated 3 months ago
- Genomic Identification of Significant Targets in Cancer (GISTIC), version 2☆51Updated 2 years ago
- Filtering of PDX samples for mouse derived reads☆27Updated 2 years ago
- Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.☆15Updated last year
- ☆24Updated last year
- Micro DNA identification☆22Updated 3 years ago
- An R package to plot maps of clone distributions in somatic evolution☆17Updated last year
- A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.☆27Updated last year
- Collection of fragmentomic analysis scripts☆11Updated 8 months ago
- ☆13Updated 7 years ago
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆42Updated this week
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 years ago
- ☆11Updated last year
- An R package to time somatic mutations☆61Updated 4 years ago
- Fork of the Polysolver project☆31Updated 5 years ago