Alternatives and similar repositories for cfDNA

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

• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 8 years 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 …
  ☆37Updated 3 years ago
• XWangLabTHU / cfDNApipe
  cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
  ☆74Updated 3 years ago
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆115Updated 8 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆133Updated last year
• raphael-group / THetA
  Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberration…
  ☆74Updated 4 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆109Updated 4 years ago
• YangLab / CIRCexplorer2
  circular RNA analysis toolset
  ☆86Updated last year
• aryeelab / guideseq
  Analysis pipeline for the GUIDE-seq assay.
  ☆80Updated 2 years ago
• bowhan / piPipes
  piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School
  ☆61Updated 5 months ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆60Updated 5 years ago
• likelet / LncPipe
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆84Updated 3 years ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated 2 years ago
• cancer-genomics / delfi_scripts
  ☆74Updated 4 years ago
• YangLab / CIRCexplorer
  A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …
  ☆62Updated 6 years ago
• dariober / bioinformatics-cafe
  Unsorted scripts for bioinformatics
  ☆61Updated 4 years ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆49Updated 6 years ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆93Updated 8 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 3 months ago
• hms-dbmi / 3d-genome-processing-tutorial
  A 3D genome data processing tutorial for ISMB/ECCB 2017
  ☆52Updated 8 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• bmvdgeijn / WASP
  WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
  ☆110Updated 4 years ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆57Updated 5 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆83Updated 10 months ago
• bioinform / rnacocktail
  ☆89Updated 5 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆122Updated 2 years ago