Basic analysis

Tools: scanpy

Usage

Run Scanpy Standard Analysis

positional arguments:
  indir                 cellranger filtered_feature_bc_matrix directory
  outdir                output directory

options:
  -h, --help            show this help message and exit
  --minGenes MINGENES   min gene counts for one cell
  --maxGenes MAXGENES   max gene counts for one cell
  --minCells MINCELLS   min cell counts for one gene
  --maxMT MAXMT         max percentage of mitochondrial
  --markerTesting MARKERTESTING
                        testing method used to find marker genes
  --focusedGenes [FOCUSEDGENES ...]
                        gene list, separated by space
  --pcNums PCNUMS       run clustering and umap with the fixed pc counts
  --neighbors NEIGHBORS
                        neighbors used to find cluster

Outputs

├── 01_after_qc.rds                        # result after qc
├── 01_qc.pdf
├── 02_normalization.rds                   # result after normalization
├── 03_feature_selection.rds               # result after feature selection
├── 03_top10_features.pdf
├── 04_scale.rds                           # result after scaling
├── 05_determine_dimensionality.pdf 
├── 05_dimension_reduction.rds             # result after dimension reduction
├── 05_pca.pdf                             # pca plot
└── 05_umap.pdf                            # umap plot