Alternatives and similar repositories for cgpPindel

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

• cancerit / ClusterSV
  SV clustering
  ☆29Updated 4 years ago
• cancerit / CaVEMan
  SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer sampl…
  ☆63Updated 3 months ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆43Updated 3 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 7 years ago
• OpenGenomics / mc3
  ☆35Updated 4 years ago
• guigolab / grape-nf
  An automated RNA-seq pipeline using Nextflow
  ☆37Updated 10 months ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆31Updated 6 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• 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…
  ☆45Updated 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.
  ☆49Updated 6 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆80Updated 2 months ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 7 years ago
• CCBR / Pipeliner
  An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
  ☆4Updated 2 years ago
• carjed / helmsman
  highly-efficient & lightweight mutation signature matrix aggregation
  ☆18Updated 3 years ago
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆38Updated 5 years ago
• gzhmat / ShinyCNV
  a Shiny/R application to view and annotate copy number variations
  ☆28Updated 2 years ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 6 months ago
• ncbi / BAMscale
  BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy …
  ☆70Updated 8 months ago
• kgori / sigfit
  Flexible Bayesian inference of mutational signatures
  ☆35Updated 2 years ago
• rhshah / iCallSV
  A Framework to call Structural Variants from NGS based datasets
  ☆22Updated 7 years ago
• gatk-workflows / gatk3-4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
  ☆51Updated 5 years ago
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆57Updated 4 months ago
• kkrizanovic / RNAseqEval
  A tool for evaluating RNA seq mapping
  ☆22Updated 6 years ago
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 years ago
• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 10 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆42Updated 4 years ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆85Updated 4 years ago