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
  ☆134Updated 2 years ago
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆153Updated last year
• MathOnco / NeoPredPipe
  Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
  ☆115Updated last year
• immunoengineer / gliph
  Grouping of Lymphocyte Interactions by Paratope Hotspots
  ☆96Updated 5 years ago
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago
• antigenomics / vdjdb-db
  🗂️ [vdjdb.com is up and running!] Git-based TCR database storage & management. Submissions welcome!
  ☆150Updated last week
• 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-…
  ☆106Updated 3 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• kundajelab / atac_dnase_pipelines
  ATAC-seq and DNase-seq processing pipeline
  ☆165Updated 3 years ago
• phbradley / tcr-dist
  Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)
  ☆86Updated 4 years ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆246Updated last week
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆119Updated 3 years ago
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆157Updated last year
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆112Updated 3 years ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆208Updated last year
• singleron-RD / CeleScope
  Single Cell Analysis Pipelines
  ☆116Updated last week
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆124Updated 5 years ago
• griffithlab / pVACtools
  ☆168Updated 3 weeks ago
• YeoLab / single-cell-bioinformatics
  Course material in notebook format for learning about single cell bioinformatics methods
  ☆100Updated 9 years ago
• crazyhottommy / pyflow-ChIPseq
  a snakemake pipeline to process ChIP-seq files from GEO or in-house
  ☆131Updated last month
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• andrewrech / antigen.garnish
  ☆48Updated 3 years ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆207Updated last year
• 10XGenomics / vartrix
  Single-Cell Genotyping Tool
  ☆215Updated 2 years ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆120Updated 3 years ago
• jernst98 / ChromHMM
  ☆95Updated 7 months ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆148Updated 3 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…
  ☆50Updated 6 months ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆236Updated last month
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆94Updated 2 years ago