Alternatives and similar repositories for toil-rnaseq:

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

• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 4 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 5 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆65Updated 5 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• CCBR / Pipeliner
  An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
  ☆4Updated last year
• AstraZeneca-NGS / disambiguate
  Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
  ☆31Updated 6 years ago
• lanagarmire / SSrGE
  ☆33Updated 5 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 2 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆49Updated 2 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆52Updated 4 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 2 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 2 months ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 3 years ago
• ding-lab / hotspot3d
  3D hotspot mutation proximity analysis tool
  ☆47Updated 2 years ago
• OpenGenomics / mc3
  ☆35Updated 4 years ago
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 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.
  ☆48Updated 5 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• kircherlab / CADD-scripts
  CADD scripts release for offline scoring. For more information about CADD, please visit our website
  ☆78Updated 4 months ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• stjude / CICERO
  CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
  ☆38Updated 3 months ago
• PGDX / cerebro-paper
  ☆23Updated 6 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• biocore-ntnu / epic
  (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
  ☆31Updated 6 years ago
• nskvir / RepEnrich
  RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆27Updated 3 years ago