/dv-pipelines

Pipelines for Analysis And Visualization

Primary LanguageNextflowMIT LicenseMIT

Nextflow pipelines for scRNA-Seq and ImmunoSeq analysis

The repository contains nextflow scripts to run different workflows for scRNA-Seq analysis as well as MiXCR workflow for AIRR-Seq data analysis. The scRNA-Seq workflows are divide into five logical steps

  1. Count matrix generation
  2. Preprocessing
  3. Clustering
  4. Cell-type classification
  5. Differential expression analysis
  6. Trajectory analysis

scRNA-Seq and AIRR-Seq tools incorporated

  1. MiXCR
  2. Monocle3
  3. Seurat
  4. Scanpy
  5. Scater
  6. Scran
  7. DropletUtils