reiterlab / treeomics
Decrypting somatic mutation patterns to reveal the evolution of cancer
☆55Updated 3 years ago
Related projects: ⓘ
- identifying mutational significance in cancer genomes☆59Updated last year
- gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (…☆32Updated 2 years ago
- ☆42Updated 5 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆59Updated 5 years ago
- Documenting usage and experience with bioinformatic tools☆39Updated 9 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆68Updated 3 months ago
- An R package to time somatic mutations☆57Updated 3 years ago
- Identifying recurrent mutations in cancer☆37Updated 3 years ago
- Burden testing against public controls☆49Updated 6 months ago
- chia pet analysis software☆24Updated 5 years ago
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆37Updated 3 years ago
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…☆53Updated 4 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…☆43Updated 2 years ago
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated last year
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆68Updated 3 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago
- ☆65Updated last year
- Battenberg R package for subclonal copynumber estimation☆77Updated last month
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated last year
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated last year
- QDNAseq package for Bioconductor☆45Updated last month
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆61Updated 4 years ago
- Quality of RNA-Seq Toolset☆52Updated 5 years ago
- ☆18Updated 2 years ago
- Public repository containing research code for the TCGA PanCanAtlas Splicing project☆41Updated 3 years ago
- Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem☆29Updated 6 years ago
- Tumor Mutational Burden☆50Updated 3 weeks ago
- ☆13Updated 7 years ago
- Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.☆68Updated 3 years ago
- Junction Based Analysis of Splicing Events for RNA-Seq☆30Updated 6 years ago