Alternatives and similar repositories for fragmentomics

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

• adoebley / Griffin
  A flexible framework for nucleosome profiling of cell-free DNA
  ☆28Updated 2 years ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆36Updated 4 months ago
• nriddiford / cnvPlotteR
  Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec
  ☆13Updated 5 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆42Updated 2 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆32Updated 2 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆30Updated 11 months ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆41Updated last year
• KhiabanianLab / All-FIT
  All-FIT - Allele-Frequency-based Imputation of Tumor Purity
  ☆18Updated 6 years ago
• ndbrown6 / MSK-GRAIL-TECHVAL
  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
  ☆22Updated 5 years ago
• sdchandra / CNAclinic
  ☆26Updated last year
• hliang / cnv-seq
  cnv-seq with custom bugfix
  ☆10Updated 12 years ago
• cphgeno / CNVbench
  Benchmarking of CNV calling tools
  ☆18Updated 6 years ago
• epifluidlab / cragr
  R package for CRAG
  ☆12Updated 11 months ago
• bioinf / caller_benchmark
  Companion repository for the human variant calling pipeline comparison paper
  ☆11Updated 3 years ago
• ENCODE-DCC / wgbs-pipeline
  ENCODE whole-genome bisulfite sequencing (WGBS) pipeline
  ☆32Updated 3 years ago
• cancer-genomics / reproduce_lucas_wflow
  ☆31Updated last year
• eyzhao / hrdetect-pipeline
  ☆36Updated 6 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆54Updated last year
• christacaggiano / celfie
  cfDNA cell type of origin estimation
  ☆34Updated 2 years ago
• hartwigmedical / pipeline5
  ☆22Updated 2 months ago
• nf-core / circdna
  Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from…
  ☆31Updated 7 months ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆65Updated 5 years ago
• ben-laufer / CpG_Me
  A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to …
  ☆24Updated 3 years ago
• hellbelly / BS-Snper
  ☆39Updated 4 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• bjtrost / TCAG-WGS-CNV-workflow
  Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods
  ☆46Updated 3 years ago
• rbundschuh / SMaSH
  A tool for sample swap identification in high throughput sequencing studies
  ☆10Updated 10 months ago
• cortes-ciriano-lab / ReConPlot
  ☆24Updated last year
• TRON-Bioinformatics / EasyFuse
  EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
  ☆62Updated last week
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 7 months ago