Alternatives and similar repositories for RNASeq

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

• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• ewels / nf-core-rnaseq
  See the main fork of this repository here >>>
  ☆38Updated last week
• 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…
  ☆52Updated 4 years ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 2 years ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆66Updated 2 weeks ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆46Updated 7 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 2 years ago
• a2iEditing / RNAEditingIndexer
  A tool for the calculation of RNA-editing index for RNA seq data
  ☆43Updated last year
• taylor-lab / hotspots
  Identifying recurrent mutations in cancer
  ☆37Updated 4 years ago
• bharani-lab / WES-Benchmarking-Pipeline_Manoj
  Benchmarking of aligners and variant callers for Whole Exome Sequencing data
  ☆19Updated 6 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆50Updated 2 years ago
• ambj / MuPeXI
  MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
  ☆50Updated 5 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆47Updated last week
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆50Updated 3 years ago
• ding-lab / PanCanAtlasGermline
  ☆44Updated 6 years ago
• alkodsi / ctDNAtools
  R package to work with ctDNA sequencing data
  ☆40Updated 3 years ago
• KarchinLab / 2020plus
  Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
  ☆49Updated 9 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 9 months ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆74Updated 9 months ago
• cancerit / BRASS
  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
  ☆57Updated 9 months ago
• broadinstitute / oncotator
  ☆68Updated 2 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆70Updated 8 months ago
• likelet / LncPipe
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆82Updated 2 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆114Updated 10 months ago