taylor-lab / hotspots
Identifying recurrent mutations in cancer
☆37Updated 4 years ago
Alternatives and similar repositories for hotspots:
Users that are interested in hotspots are comparing it to the libraries listed below
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆44Updated 2 years ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 7 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 7 years ago
- ☆68Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- Multi-sample somatic variant caller☆50Updated 3 years ago
- QDNAseq package for Bioconductor☆50Updated 9 months ago
- gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (…☆33Updated 3 years ago
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆42Updated 3 years ago
- R package for bcbio RNA-seq analysis.☆62Updated 7 months ago
- OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data☆52Updated 3 weeks ago
- Run Picard on BAM files and collate 90 metrics into one file.☆41Updated 7 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Updated 4 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated last month
- A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.☆35Updated 3 years ago
- Battenberg algorithm and associated implementation script☆52Updated 4 years ago
- Filtering of PDX samples for mouse derived reads☆27Updated 2 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆50Updated 2 years ago
- Decrypting somatic mutation patterns to reveal the evolution of cancer☆56Updated 4 years ago
- RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code …☆55Updated 12 years ago
- ☆44Updated 6 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated 2 years ago
- Public repository containing research code for the TCGA PanCanAtlas Splicing project☆41Updated 4 years ago
- ChIP-seq DC and QC Pipeline☆34Updated 4 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆71Updated 11 months ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆39Updated 3 years ago
- ☆30Updated 6 years ago
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago