cancerit / alleleCountLinks
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 allele [ACGT] at that location (given any filter settings)
☆44Updated 3 years ago
Alternatives and similar repositories for alleleCount
Users that are interested in alleleCount are comparing it to the libraries listed below
Sorting:
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 7 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆72Updated last year
- deepStats: a stastitical toolbox for deeptools and genomic signals☆35Updated 4 years ago
- ☆36Updated 6 years ago
- An R package for predicting HR deficiency from mutation contexts☆30Updated 11 months ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆31Updated 10 months ago
- DriverPower☆26Updated last year
- OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data☆56Updated 3 months ago
- Decrypting somatic mutation patterns to reveal the evolution of cancer☆56Updated 4 years ago
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Updated 6 years ago
- Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…☆42Updated last year
- A comprehensive toolkit for mutational signature analysis☆41Updated last year
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 3 years ago
- Identifying recurrent mutations in cancer☆39Updated 4 years ago
- DNA copy number detection from off-target sequence data☆33Updated 7 years ago
- Filters for false-positive mutation calls in NGS☆34Updated 6 years ago
- ☆35Updated 5 years ago
- ☆33Updated 3 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆40Updated 4 years ago
- DRAGEN Tumor/Normal workflow post-processing☆25Updated 2 years ago
- A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.☆37Updated 4 years ago
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆42Updated 5 months ago
- 📊Evaluating, filtering, comparing, and visualising VCF☆28Updated 2 years ago
- Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests☆50Updated last year
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆35Updated last year
- Tutorials covering various topics in genomic data analysis.☆16Updated 7 years ago
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆77Updated 3 weeks ago
- Gene Fusion Visualiser☆51Updated 3 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆32Updated 2 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆30Updated 7 years ago