Alternatives and similar repositories for cfDNA

Users that are interested in cfDNA are comparing it to the libraries listed below

• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆83Updated 7 years ago
• FoundationMedicineInc / SGZ
  ☆41Updated last year
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 5 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 11 months ago
• dinhdiep / MONOD2
  MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
  ☆39Updated 6 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• XWangLabTHU / cfDNApipe
  cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
  ☆67Updated 2 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated 9 months ago
• hw538 / cfDNAPro
  cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
  ☆33Updated this week
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 7 months ago
• kircherlab / CADD-scripts
  CADD scripts release for offline scoring. For more information about CADD, please visit our website
  ☆82Updated last month
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆53Updated 4 years ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆71Updated 7 years ago
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆109Updated 2 months ago
• YangLab / CIRCexplorer
  A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …
  ☆61Updated 6 years ago
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆46Updated last year
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆37Updated 7 years ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆48Updated 6 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆59Updated 9 months ago
• nloyfer / meth_atlas
  ☆48Updated 3 years ago
• likelet / LncPipe
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆82Updated 2 years ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 4 months ago
• dieterich-lab / DCC
  DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …
  ☆36Updated 2 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago