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
• gtrichard / deepStats
  deepStats: a stastitical toolbox for deeptools and genomic signals
  ☆35Updated 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
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 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…
  ☆45Updated 3 years ago
• 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 This tool has been superseded by https://github.com/griffithlab/pVACtools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
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆36Updated 3 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆42Updated 4 years ago
• taylor-lab / hotspots
  Identifying recurrent mutations in cancer
  ☆39Updated 4 years ago
• stjude / CICERO
  CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
  ☆41Updated 2 weeks ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• astrazeneca-cgr-publications / JARVIS
  JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes
  ☆23Updated 10 months ago
• nskvir / RepEnrich
  RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆28Updated 3 years ago
• AstraZeneca-NGS / disambiguate
  Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
  ☆31Updated 7 years ago
• thelovelab / rnaseqDTU
  RNA-seq workflow: differential transcript usage
  ☆23Updated 2 years ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 3 years ago
• broadinstitute / gtex-viz
  GTEx Visualizations
  ☆65Updated 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
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated last year
• biocore-ntnu / epic
  (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
  ☆31Updated 7 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆84Updated 4 years ago
• pinellolab / haystack_bio
  Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
  ☆47Updated 3 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 8 years ago
• czbiohub-sf / cerebra
  A tool for fast and accurate summarizing of variant calling format (VCF) files
  ☆61Updated 2 years ago