Alternatives and similar repositories for fragmentomics

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

• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆35Updated 3 months ago
• adoebley / Griffin
  A flexible framework for nucleosome profiling of cell-free DNA
  ☆28Updated 2 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆32Updated 2 years ago
• WGLab / CancerVar
  Clinical interpretation of somatic mutations in cancer
  ☆50Updated 10 months ago
• cancer-genomics / reproduce_lucas_wflow
  ☆31Updated last year
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆42Updated last year
• hartwigmedical / pipeline5
  ☆21Updated last month
• sdchandra / CNAclinic
  ☆26Updated last year
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆30Updated 10 months ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆65Updated 5 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆57Updated last week
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆42Updated 2 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• nriddiford / cnvPlotteR
  Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec
  ☆13Updated 5 years ago
• hliang / cnv-seq
  cnv-seq with custom bugfix
  ☆10Updated 12 years ago
• eyzhao / hrdetect-pipeline
  ☆36Updated 6 years ago
• cphgeno / CNVbench
  Benchmarking of CNV calling tools
  ☆18Updated 6 years ago
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 3 years ago
• AlexandrovLab / SigProfilerPlotting
  SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational pattern…
  ☆52Updated 2 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆53Updated last year
• KhiabanianLab / All-FIT
  All-FIT - Allele-Frequency-based Imputation of Tumor Purity
  ☆18Updated 6 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆63Updated 5 months ago
• TRON-Bioinformatics / EasyFuse
  EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
  ☆62Updated 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 6 months ago
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆51Updated 2 months ago
• mhalushka / miRge3.0
  Comprehensive analysis of small RNA sequencing data
  ☆34Updated 7 months ago
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆44Updated 3 years ago
• ndbrown6 / MSK-GRAIL-TECHVAL
  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
  ☆22Updated 5 years ago