shendurelab / cfDNA
Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA
☆67Updated 4 years ago
Alternatives and similar repositories for cfDNA:
Users that are interested in cfDNA are comparing it to the libraries listed below
- Reference data: BED files, genes, transcripts, variations.☆82Updated 7 years ago
- ☆40Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 3 years ago
- MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data☆38Updated 6 years ago
- A pipeline for analyzing DNA methylation data from bisulfite sequencing.☆70Updated 2 years ago
- A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …☆60Updated 5 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆77Updated 5 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- tools to find circRNAs in RNA-seq data☆42Updated 7 years ago
- Relevant papers for CNV and SV approaches☆94Updated 4 months ago
- cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data☆63Updated 2 years ago
- Software program for checking sample matching for NGS data☆128Updated 8 months ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆52Updated 4 years ago
- QDNAseq package for Bioconductor☆49Updated 7 months ago
- A tool for bigWig files.☆119Updated 6 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- nucleosome calling using ATAC-seq☆106Updated 4 years ago
- Allele-specific alignment sorting☆54Updated 2 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- Tumor Mutational Burden☆58Updated 6 months ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- ☆89Updated 4 years ago
- Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data☆82Updated last month
- ☆21Updated this week
- A simplified pipeline for ctDNA sequencing data analysis☆36Updated 7 years ago
- Microsatellite instability (MSI) detection for tumor only data.☆101Updated 10 months ago
- WisecondorX — An evolved WISECONDOR☆96Updated 5 months ago
- Microsatellite Instability (MSI) detection using high-throughput sequencing data.☆106Updated last week
- ☆78Updated 11 years ago
- WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR): Detect fetal trisomies and smaller CNV's in a maternal plasma sample using wh…☆44Updated 10 months ago