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trajectory inference
Sue9104 edited this page Nov 1, 2022
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Tools: scVelo
scrna-trajectory <indir> <outdir> <h5ad> <gtf>
Run trajectory analysis with scVelo
positional arguments:
indir cellranger directory, including outs and outs/analysis
outdir output directory
h5ad seurat object h5ad file
gtf gene gtf file, which is located in ref_folder/genes/genes.gtf
options:
-h, --help show this help message and exit
--genes [GENES ...] gene list, seprate by space
--mode MODE stochastic or dynamical
--start START barcode for start cell
Two packages are included: scrnaRecom (R) and pyscrnarecom (Python)
Add library path to PATH
Excutable commands are available under the scrnaRecom/exec folder after installation.
Excutable commands are available under the current environment after installation.