integration - WXlab-NJMU/scrna-recom GitHub Wiki
Tools: Seurat CCA, Seurat RPCA, Liger, Harmony
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)]
correct-batch.R examples/input.rds ~/tests/integraion pbmc
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