ChristofferFlensburg / superFreq
Analysis pipeline for cancer sequencing data
☆110Updated 4 months ago
Related projects ⓘ
Alternatives and complementary repositories for superFreq
- An R package for inferring the subclonal architecture of tumors☆115Updated last year
- Battenberg algorithm and associated implementation script☆52Updated 4 years ago
- R package for extracting and visualizing mutational patterns in base substitution catalogues☆104Updated 2 years ago
- R package designed to simplify structural variant analysis☆70Updated 2 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆69Updated 4 years ago
- R package for bcbio RNA-seq analysis.☆58Updated 2 months ago
- Collection of CGAT NGS Pipelines☆43Updated 6 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆94Updated 3 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆69Updated 5 months ago
- Transcript quantification import for modular pipelines☆136Updated 7 months ago
- phasing and Allele Specific Expression from RNA-seq☆111Updated 4 months ago
- R package containing useful functions for mutational signature analysis☆80Updated this week
- Copy number calling and variant classification using targeted short read sequencing☆128Updated this week
- Battenberg R package for subclonal copynumber estimation☆82Updated last week
- Quality of RNA-Seq Toolset☆52Updated 5 years ago
- Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.☆57Updated 4 months ago
- 🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips☆62Updated 2 weeks ago
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆142Updated 4 years ago
- Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.☆121Updated 3 months ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- deconstructSigs☆139Updated last year
- Genomic Interactive Visualization Engine☆145Updated last year
- fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome☆143Updated 2 months ago
- Microassembly based somatic variant caller for NGS data☆154Updated 2 years ago
- ☆78Updated 10 years ago
- ☆65Updated last year
- Microsatellite instability (MSI) detection for tumor only data.☆94Updated 6 months ago
- Run Picard on BAM files and collate 90 metrics into one file.☆39Updated 7 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆50Updated 4 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆76Updated 4 years ago