Alternatives and similar repositories for PDX-Analysis-Workflows

Users that are interested in PDX-Analysis-Workflows are comparing it to the libraries listed below

• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• LukszaLab / NeoantigenEditing
  ☆17Updated 3 years ago
• tianshilu / QBRC-Neoantigen-Pipeline
  QBRC Neoantigen calling pipeline with CSiN calculation embedded
  ☆24Updated 3 years ago
• interactivereport / xOmicsShiny
  xOmicsShiny: an R Shiny application for cross-omics data analysis and pathway mapping, Bioinformatics Advances, Volume 5, Issue 1, 2025, …
  ☆31Updated last week
• icbi-lab / NeoFuse
  NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
  ☆19Updated 3 years ago
• fusiontranscripts / FusionBenchmarking
  Toolkit for benchmarking fusion transcript predictions
  ☆19Updated 11 months ago
• icbi-lab / downloader
  Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)
  ☆9Updated 4 months ago
• snakemake-workflows / dna-seq-neoantigen-prediction
  Snakemake workflow for neoantigen prediction
  ☆14Updated last year
• BGI2016 / PSSMHCpan
  A novel PSSM based software for predicting class I peptide-HLA binding affinity
  ☆17Updated 8 years ago
• chess-genome / chess
  Comprehensive Human Expressed SequenceS
  ☆18Updated 3 weeks ago
• jiujiezz / tsnad
  Detecting somatic mutations and predicting tumor-specific neo-antigens
  ☆29Updated 3 years ago
• XSLiuLab / Seq2Neo
  Seq2Neo: a comprehensive pipeline for cancer neoantigen immunogenicity prediction
  ☆21Updated 2 years ago
• zqfang / snakeflow
  bioinfo workflow based on snakemake
  ☆13Updated last year
• khuranalab / CompositeDriver
  Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
  ☆15Updated 6 years ago
• pdxgx / neoepiscope
  predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data
  ☆27Updated last year
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆31Updated 3 years ago
• mandricigor / imrep
  ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
  ☆28Updated 5 years ago
• antigenomics / vdjmatch
  ⚙️ Matching T-cell repertoire against a database of TCR antigen specificities
  ☆38Updated 6 years ago
• slowkow / cellguide
  🧭 Navigate single-cell RNA-seq datasets in your web browser.
  ☆29Updated 2 years ago
• OSU-BMBL / IRIS
  A Shiny web server for interactive visualization and analysis of RNA-seq data
  ☆22Updated 4 years ago
• gagneurlab / FRASER-analysis
  Accompanying analysis code for the FRASER manuscript
  ☆26Updated 4 years ago
• SimoneTiberi / BANDITS
  BANDITS: Bayesian ANalysis of DIfferenTial Splicing
  ☆18Updated last year
• ShixiangWang / Variants2Neoantigen
  A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
  ☆29Updated 5 years ago
• jfjlaros / demultiplex
  Versatile FASTA/FASTQ demultiplexer.
  ☆33Updated last year
• uio-bmi / compairr
  Comparison of Adaptive Immune Receptor Repertoires
  ☆27Updated 6 months ago
• KirstLab / asc_seurat
  ☆24Updated last year
• mikelove / zinbwave-deseq2
  Workflow for ZINB-WaVE + DESeq2 intergration for single-cell RNA-seq
  ☆31Updated 4 years ago
• Xinglab / IRIS
  IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening
  ☆25Updated 11 months ago
• erhard-lab / grandR
  R package for nucleotide conversion sequencing data analysis
  ☆13Updated 5 months ago
• aertslab / GENIE3
  GENIE3 (GEne Network Inference with Ensemble of trees) R-package
  ☆33Updated 3 years ago