integration

Integration

Tools: Seurat CCA, Seurat RPCA, Liger, Harmony

Usages

correct-batch.R <input> <outdir> <project> [options] 


scRNA-seq Batch Correction using Seurat, Liger or Harmony

positional arguments:
  input             input SeuratObject rds file
  outdir            output result folder
  project           project name

flags:
  -h, --help        show this help message and exit

optional arguments:
  -m, --method      SeuratCCA, SeuratRPCA, Harmony, Liger [default: SeuratCCA]
  -d, --dim         feature nums, npc in Seurat::RunPCA or k in rliger::optimizeALS, default is 30 [default: 30]
  -n, --nfeatures   number of variable features to use for scaledata and pca, default is 2000 [default: 2000]
  -k, --kparam      k.param of knn in FindNeighbor, default is 20
                    [default: 20]
  -r, --resolution  resolution of cluster, default is 0.8 [default: 0.8]
  -p, --plot        features to plot on umap [default: (nFeature_RNA,percent.mt,percent.rb)]

Examples

correct-batch.R examples/input.rds ~/tests/integraion pbmc

Outputs

integraion
├── pbmc.debatch.harmony.dim=30.pdf         # harmony integration figures 
├── pbmc.debatch.harmony.dim=30.rds         # harmony integration results 
├── pbmc.debatch.liger.dim=30.pdf           # liger integration figures 
├── pbmc.debatch.liger.dim=30.rds           # liger integration results
├── pbmc.debatch.seurat-cca.dim=30.pdf      # seurat cca integration figures 
└── pbmc.debatch.seurat-cca.dim=30.rds      # seurat cca integration results