Alternatives and similar repositories for NGSCheckMate

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

• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 months ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆111Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆155Updated 2 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
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆107Updated 2 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 4 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆172Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 7 years ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 5 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆191Updated 2 months ago
• sztup / scarHRD
  ☆117Updated 2 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆128Updated 3 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆140Updated 2 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆115Updated last month
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆151Updated 3 months ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆49Updated 6 years ago
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆113Updated 7 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆147Updated 3 months ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆156Updated last week
• Xinglab / rmats2sashimiplot
  ☆153Updated 5 months ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆120Updated 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…
  ☆55Updated 5 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago