Alternatives and similar repositories for toil-rnaseq

Users that are interested in toil-rnaseq are comparing it to the libraries listed below

• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆36Updated 4 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
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆43Updated 4 years ago
• KarchinLab / 2020plus
  Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
  ☆50Updated last year
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 years ago
• gtrichard / deepStats
  deepStats: a stastitical toolbox for deeptools and genomic signals
  ☆35Updated 4 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 3 years ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years 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
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 4 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• christacaggiano / celfie
  cfDNA cell type of origin estimation
  ☆34Updated 2 years ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 4 years ago
• broadinstitute / gtex-viz
  GTEx Visualizations
  ☆66Updated 4 years ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆30Updated 6 years ago
• ambj / MuPeXI
  MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
  ☆52Updated 6 years ago
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆79Updated 7 months ago
• czbiohub-sf / cerebra
  A tool for fast and accurate summarizing of variant calling format (VCF) files
  ☆61Updated 3 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 8 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆40Updated 4 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆30Updated 11 months ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 7 years ago
• yuchaojiang / Canopy
  Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
  ☆70Updated 4 years ago
• ding-lab / hotspot3d
  3D hotspot mutation proximity analysis tool
  ☆52Updated 2 years ago