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Merge branch 'master' of github.com:calico/solo
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njbernstein committed Jun 30, 2021
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Expand Up @@ -17,40 +17,42 @@ If you don't have conda follow the instructions here: https://docs.conda.io/proj

### How to solo
```
usage: solo [-h] [-d DOUBLET_DEPTH] [-g] [-o OUT_DIR] [-r DOUBLET_RATIO]
[-s SEED] [-k KNOWN_DOUBLETS] [-t {multinomial,average,sum}]
[-e EXPECTED_NUMBER_OF_DOUBLETS] [-p]
model_json_file data_file
positional arguments:
model_json_file json file to pass VAE parameters
data_file path to h5ad, loom or 10x directory containing cell by
genes counts
usage: solo [-h] -j MODEL_JSON_FILE -d DATA_PATH
[--set-reproducible-seed REPRODUCIBLE_SEED]
[--doublet-depth DOUBLET_DEPTH] [-g] [-a] [-o OUT_DIR]
[-r DOUBLET_RATIO] [-s SEED] [-e EXPECTED_NUMBER_OF_DOUBLETS] [-p]
[-recalibrate_scores] [--version]
optional arguments:
-h, --help show this help message and exit
-d DOUBLET_DEPTH Depth multiplier for a doublet relative to the average
-j MODEL_JSON_FILE json file to pass VAE parameters (default: None)
-d DATA_PATH path to h5ad, loom, or 10x mtx dir cell by genes
counts (default: None)
--set-reproducible-seed REPRODUCIBLE_SEED
Reproducible seed, give an int to set seed (default:
None)
--doublet-depth DOUBLET_DEPTH
Depth multiplier for a doublet relative to the average
of its constituents (default: 2.0)
-g Run on GPU (default: True)
-a output modified anndata object with solo scores Only
works for anndata (default: False)
-o OUT_DIR
-r DOUBLET_RATIO Ratio of doublets to true cells (default: 2.0)
-r DOUBLET_RATIO Ratio of doublets to true cells (default: 2)
-s SEED Path to previous solo output directory. Seed VAE
models with previously trained solo model. Directory
structure is assumed to be the same as solo output
directory structure. should at least have a vae.pt a
pickled object of vae weights and a latent.npy an
np.ndarray of the latents of your cells. (default:
None)
-k KNOWN_DOUBLETS Experimentally defined doublets tsv file. Should be a
single column of True/False. True indicates the cell
is a doublet. No header. (default: None)
-t {multinomial,average,sum}
Please enter multinomial, average, or sum (default:
multinomial)
-e EXPECTED_NUMBER_OF_DOUBLETS
Experimentally expected number of doublets (default:
None)
-p Plot outputs (default: True)
-p Plot outputs for solo (default: False)
-recalibrate_scores Recalibrate doublet scores (not recommended anymore)
(default: False)
--version Get version of solo-sc (default: False)
```

Warning: If you are going directly from cellranger 10x output you may want to manually inspect your data prior to running solo.
Expand All @@ -71,11 +73,11 @@ model_json example:

Outputs:
* `is_doublet.npy` np boolean array, true if a cell is a doublet, differs from `preds.npy` if `-e expected_number_of_doublets` parameter was used
* `vae.pt` scVI weights for vae
* `classifier.pt` scVI weights for classifier
* `vae` scVI directory for vae
* `classifier.pt` scVI directory for classifier
* `latent.npy` latent embedding for each cell
* `preds.npy` doublet predictions
* `softmax_scores.npy` updated softmax of doublet scores (see paper)
* `softmax_scores.npy` updated softmax of doublet scores (see paper), same as `no_update_softmax_scores.npy` now
* `no_update_softmax_scores.npy` raw softmax of doublet scores

* `logit_scores.npy` logit of doublet scores
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