README.md

this repository is archived as this functionality is now in cellxgene

cellxgene-prepare

CLI for preprocessing data for use with cellxgene

usage

Prepare a dataset example.h5ad by calling

cellxgene-prepare example.h5ad --engine=scanpy --output=example_processed.h5ad

This will save a new file example_processed.h5ad with a few new fields prepared designed for use with the specified engine.

Several options are available for specifying preprocessing, generating and saving plots, ensuring data sparsity, and others, to see all options call

cellxgene --help

Options:
  --engine [scanpy]               computational engine  [default: scanpy]
  --format [h5ad|10x_mtx|loom]    data format  [default: h5ad]
  --layout [umap|tsne|umap+tsne]  layout algorithm  [default: umap]
  --recipe [none|seurat|zheng17]  preprocessing receipe to run  [default:
                                  none]
  --output TEXT                   whether or not to save a new file
  --sparse / --no-sparse          whether to require sparsity
  --plotting / --no-plotting      whether or not to generate plots
  --help                          Show this message and exit.

development

For development and testing purposes, just install the requirements into your Python environment, and call

python prepare/cli.py example.h5ad

to simulate launching the CLI