chrisamiller / readDepth

Related projects ⓘ

Alternatives and complementary repositories for readDepth

• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆28Updated 6 years ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆33Updated last year
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 4 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆32Updated 9 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆48Updated 3 months ago
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆22Updated 3 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆24Updated 8 years ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 6 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆45Updated 2 weeks ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆65Updated 2 months ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆45Updated 6 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆36Updated 2 years ago
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆21Updated last year
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆43Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆77Updated 8 months ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆31Updated 8 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 2 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆48Updated 5 years ago
• CshlSiepelLab / LINSIGHT
  ☆24Updated 5 months ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 5 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆54Updated 10 months ago
• ken0-1n / Genomon-ITDetector
  for detecting internal tandem duplication from genome sequence data.
  ☆11Updated 5 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 2 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 5 years ago
• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆69Updated 2 years ago
• molgenis / capice
  ☆23Updated 2 months ago