├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.md ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── celltypist ├── __init__.py ├── annotate.py ├── classifier.py ├── command_line.py ├── data │ └── samples │ │ ├── Ensembl105_Human2Mouse_Genes.csv │ │ ├── Ensembl110_Cynomolgus2Mouse_Genes.csv │ │ ├── Ensembl110_Cynomolgus2Pig_Genes.csv │ │ ├── Ensembl110_Cynomolgus2Rhesus_Genes.csv │ │ ├── Ensembl110_Human2Cynomolgus_Genes.csv │ │ ├── Ensembl110_Human2Pig_Genes.csv │ │ ├── Ensembl110_Human2Rhesus_Genes.csv │ │ ├── Ensembl110_Pig2Mouse_Genes.csv │ │ ├── Ensembl110_Rhesus2Mouse_Genes.csv │ │ ├── Ensembl110_Rhesus2Pig_Genes.csv │ │ ├── GENCODEv44_Gene_id2name.csv │ │ └── sample_cell_by_gene.csv ├── logger.py ├── models.py ├── plot.py ├── samples.py └── train.py ├── docs ├── Makefile ├── notebook │ ├── celltypist_tutorial.ipynb │ ├── celltypist_tutorial_cv.ipynb │ └── celltypist_tutorial_ml.ipynb ├── requirements.txt └── source │ ├── _static │ └── img │ │ └── logo_celltypist.png │ ├── celltypist.annotate.rst │ ├── celltypist.classifier.AnnotationResult.rst │ ├── celltypist.classifier.Classifier.rst │ ├── celltypist.dotplot.rst │ ├── celltypist.models.Model.rst │ ├── celltypist.models.download_models.rst │ ├── celltypist.samples.downsample_adata.rst │ ├── celltypist.train.rst │ ├── conf.py │ ├── index.rst │ └── notebook ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/CITATION.cff -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/README.md -------------------------------------------------------------------------------- /celltypist/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/__init__.py -------------------------------------------------------------------------------- /celltypist/annotate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/annotate.py -------------------------------------------------------------------------------- /celltypist/classifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/classifier.py -------------------------------------------------------------------------------- /celltypist/command_line.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/command_line.py -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl105_Human2Mouse_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl105_Human2Mouse_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Cynomolgus2Mouse_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Cynomolgus2Mouse_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Cynomolgus2Pig_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Cynomolgus2Pig_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Cynomolgus2Rhesus_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Cynomolgus2Rhesus_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Human2Cynomolgus_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Human2Cynomolgus_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Human2Pig_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Human2Pig_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Human2Rhesus_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Human2Rhesus_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Pig2Mouse_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Pig2Mouse_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Rhesus2Mouse_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Rhesus2Mouse_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/Ensembl110_Rhesus2Pig_Genes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/Ensembl110_Rhesus2Pig_Genes.csv -------------------------------------------------------------------------------- /celltypist/data/samples/GENCODEv44_Gene_id2name.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/GENCODEv44_Gene_id2name.csv -------------------------------------------------------------------------------- /celltypist/data/samples/sample_cell_by_gene.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/data/samples/sample_cell_by_gene.csv -------------------------------------------------------------------------------- /celltypist/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/logger.py -------------------------------------------------------------------------------- /celltypist/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/models.py -------------------------------------------------------------------------------- /celltypist/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/plot.py -------------------------------------------------------------------------------- /celltypist/samples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/samples.py -------------------------------------------------------------------------------- /celltypist/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/celltypist/train.py -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/notebook/celltypist_tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/notebook/celltypist_tutorial.ipynb -------------------------------------------------------------------------------- /docs/notebook/celltypist_tutorial_cv.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/notebook/celltypist_tutorial_cv.ipynb -------------------------------------------------------------------------------- /docs/notebook/celltypist_tutorial_ml.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/notebook/celltypist_tutorial_ml.ipynb -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/source/_static/img/logo_celltypist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/_static/img/logo_celltypist.png -------------------------------------------------------------------------------- /docs/source/celltypist.annotate.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.annotate.rst -------------------------------------------------------------------------------- /docs/source/celltypist.classifier.AnnotationResult.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.classifier.AnnotationResult.rst -------------------------------------------------------------------------------- /docs/source/celltypist.classifier.Classifier.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.classifier.Classifier.rst -------------------------------------------------------------------------------- /docs/source/celltypist.dotplot.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.dotplot.rst -------------------------------------------------------------------------------- /docs/source/celltypist.models.Model.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.models.Model.rst -------------------------------------------------------------------------------- /docs/source/celltypist.models.download_models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.models.download_models.rst -------------------------------------------------------------------------------- /docs/source/celltypist.samples.downsample_adata.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.samples.downsample_adata.rst -------------------------------------------------------------------------------- /docs/source/celltypist.train.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/celltypist.train.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/notebook: -------------------------------------------------------------------------------- 1 | ../notebook/ -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Teichlab/celltypist/HEAD/setup.py --------------------------------------------------------------------------------