Part I sEVs recognizing

Here, we used data in github tests directory as an example, and shown how SEVtras recognizing sEVs in scRNA-seq datasets. We have generated test data in h5ad format in github, and SEVtras also supports 10x_mtx and h5 data formats.

Note1: The input droplet-gene matrix for SEVtras should be the raw data in this part; herein, the matrix should come from the raw_feature_bc_matrix directory in Cell Ranger outs.

Note2: This part requires parallel processing using the multiprocessing package. This package is currently not compatible with certain version of WSL on Windows 10. Running this part in Linux is preferred.

Note3: We don’t recommend recognizing sEVs with a single sample. Inputting more similar samples would lead to more reliable results.

We support two file input ways to run sEVs recognizing:

##1 if samples locate in one directory
import SEVtras
SEVtras.sEV_recognizer(input_path='./tests', sample_file='./tests/sample_file', out_path='./outputs', species='Homo')

The first parameter was the path of directory that contains all samples. Because these test files exists in our tests directory, so we used ./tests. The second parameter was the name of each sample in th directory row by row. If your data format is 10x_mtx, SEVtras can automatically detect the directory of sample/outs/raw_feature_bc_matrix/ (see parameter dir_origin).

out_path defines the output of SEVtras that is one h5ad file, named raw_SEVtras.h5ad, with SEVtras score (‘score’) and sEV classification (‘sEV’) in the obs for all droplets, and one named sEVs_SEVtras.h5ad with only sEV-containing droplets.

And species represents the species from which the sample was sequenced.

If samples locate in differet directories, we also supports another way to run SEVtras.

##2 if samples locate in differet directories
import SEVtras
SEVtras.sEV_recognizer(sample_file='./tests/sample_file', out_path='./outputs', species='Homo')

Here, first parameter was the abosulte path of each sample row by row.

The result of sEV_recognizer can be displayed as follows: