Alternatives and similar repositories for vdjtools:

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

• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆126Updated last year
• antigenomics / vdjdb-db
  🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!
  ☆135Updated last week
• immunoengineer / gliph
  Grouping of Lymphocyte Interactions by Paratope Hotspots
  ☆91Updated 4 years ago
• MathOnco / NeoPredPipe
  Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
  ☆110Updated 6 months ago
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆126Updated 7 months ago
• mhorlbeck / ScreenProcessing
  ☆64Updated last year
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 4 years ago
• YeoLab / single-cell-bioinformatics
  Course material in notebook format for learning about single cell bioinformatics methods
  ☆102Updated 8 years ago
• phbradley / tcr-dist
  Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)
  ☆81Updated 3 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆142Updated last year
• dviraran / xCell
  Cell types enrichment analysis
  ☆194Updated 9 months ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆298Updated last week
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆219Updated 3 months ago
• snakemake-workflows / single-cell-rna-seq
  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  ☆101Updated 2 years ago
• TRON-Bioinformatics / seq2HLA
  In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq f…
  ☆48Updated last year
• nsalomonis / altanalyze
  AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-…
  ☆100Updated 2 years ago
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆89Updated last year
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• YeoLab / eCLIP
  ☆37Updated 2 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆169Updated 8 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated this week
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆196Updated last year
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆190Updated 2 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 3 years ago
• broadinstitute / Drop-seq
  Java tools for analyzing Drop-seq data
  ☆125Updated last month
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆136Updated last year
• singleron-RD / CeleScope
  Single Cell Analysis Pipelines
  ☆97Updated last week
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆108Updated 2 years ago