cancerit / alleleCount
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)
☆43Updated 2 years ago
Alternatives and similar repositories for alleleCount:
Users that are interested in alleleCount are comparing it to the libraries listed below
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 6 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 6 years ago
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆45Updated this week
- An R package for predicting HR deficiency from mutation contexts☆28Updated last month
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆70Updated 9 months ago
- DriverPower☆26Updated last month
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated 5 months ago
- ☆34Updated 5 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 3 weeks ago
- Gene Fusion Visualiser☆51Updated 2 years ago
- ☆18Updated 3 years ago
- OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data☆49Updated last week
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 3 years ago
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆65Updated 4 years ago
- 📊Evaluating, filtering, comparing, and visualising VCF☆27Updated 2 years ago
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Updated 5 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 2 years ago
- Identifying recurrent mutations in cancer☆37Updated 4 years ago
- chia pet analysis software☆25Updated 6 years ago
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated 3 months ago
- QDNAseq package for Bioconductor☆49Updated 7 months ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…☆27Updated last year
- Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data☆27Updated last year
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- Burden testing against public controls☆50Updated last year
- CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.☆36Updated 2 months ago