OpenGene / ctdna-pipeline
A simplified pipeline for ctDNA sequencing data analysis
☆36Updated 7 years ago
Related projects ⓘ
Alternatives and complementary repositories for ctdna-pipeline
- ☆38Updated 9 months ago
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- ☆35Updated 3 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 method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆33Updated 4 months ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆94Updated 3 years ago
- ☆37Updated last year
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- ☆50Updated last year
- SMN1 copy-number and sequence variant analysis from next generation sequencing data☆22Updated last year
- ☆45Updated 5 years ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆55Updated 4 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- CN-Learn☆29Updated 4 years ago
- Tumor Mutational Burden☆55Updated 2 months ago
- Microsatellite instability (MSI) detection for cfDNA samples.☆18Updated 3 years ago
- CNV screening and annotation tool☆24Updated 8 years ago
- cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data☆60Updated 2 years ago
- tools to find circRNAs in RNA-seq data☆40Updated 7 years ago
- Burden testing against public controls☆50Updated 8 months ago
- Fork of the Polysolver project☆30Updated 5 years ago
- MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data☆35Updated 5 years ago
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆45Updated 2 years ago
- ☆88Updated 4 years ago
- QDNAseq package for Bioconductor☆48Updated 3 months ago
- Microsatellite instability (MSI) detection for tumor only data.☆94Updated 6 months ago