├── .dockerignore ├── .git-blame-ignore-revs ├── .gitattributes ├── .github └── ISSUE_TEMPLATE │ ├── bug-error-report.md │ └── no-questions-here-please-.md ├── .gitignore ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── conf.py ├── faq.rst ├── index.rst ├── installation.rst ├── releasenotes.rst └── tutorial.rst ├── notebooks ├── data │ ├── GSE60361.annotations.csv │ ├── GSE60361.genes_x_cells.tsv.gz │ ├── GSE60361.motifs.csv.gz │ └── README.txt ├── pySCENIC - AUCell example.ipynb ├── pySCENIC - Assess AUCell implementation.ipynb ├── pySCENIC - Benchmarking of different implementations for pruning.ipynb ├── pySCENIC - Comparison to R implementation of the pipeline.ipynb ├── pySCENIC - Conversion to feather of gene-based dm6 database.ipynb ├── pySCENIC - Create loom file.ipynb ├── pySCENIC - Full pipeline.ipynb ├── pySCENIC - Integration with scanpy.ipynb ├── pySCENIC - List of Transcription Factors.ipynb ├── pySCENIC - Percentiles as threshold for modules.ipynb ├── pySCENIC - Preliminary - Known TFs for Mus musculus as MGI symbols.ipynb └── pySCENIC - Test new module creation defaults.ipynb ├── pypi.sh ├── pyscenic_with_scanpy.Dockerfile ├── requirements.doc.txt ├── requirements.txt ├── requirements_docker_with_scanpy.txt ├── resources ├── allTFs_dmel.txt ├── hs_hgnc_curated_tfs.txt ├── hs_hgnc_tfs.txt ├── lambert2018.txt └── mm_mgi_tfs.txt ├── runtox.sh ├── scripts ├── cli_test_script.sh ├── fabfile.py ├── hpc-grnboost.ini ├── hpc-grnboost.py ├── hpc-modules.py ├── hpc-prune.ini └── hpc-prune.py ├── setup.cfg ├── setup.py ├── src ├── pyscenic │ ├── __init__.py │ ├── _version.py │ ├── aucell.py │ ├── binarization.py │ ├── cli │ │ ├── __init__.py │ │ ├── arboreto_with_multiprocessing.py │ │ ├── csv2loom.py │ │ ├── pyscenic.py │ │ └── utils.py │ ├── export.py │ ├── featureseq.py │ ├── log.py │ ├── math.py │ ├── plotting.py │ ├── prune.py │ ├── rss.py │ ├── transform.py │ └── utils.py └── resources │ ├── __init__.py │ ├── delineations │ ├── __init__.py │ ├── hg19-limited-upstream10000-tss-downstream10000-full-transcript.bed.gz │ ├── hg19-limited-upstream500.bed.gz │ └── hg19-limited-upstream5000-tss-downstream5000-full-transcript.bed.gz │ ├── scenic.args.txt │ └── tests │ ├── GSE103322.em.hgnc.sample.cxg.csv │ ├── __init__.py │ ├── c6.all.v6.1.symbols.gmt │ ├── hg19-tss-centered-10kb-10species.mc9nr.feather │ └── hg19-tss-centered-5kb-10species.mc9nr.db ├── tests ├── test_aucell.py ├── test_featureseq.py └── test_math.py ├── tox.ini └── versioneer.py /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aertslab/pySCENIC/HEAD/.dockerignore -------------------------------------------------------------------------------- /.git-blame-ignore-revs: -------------------------------------------------------------------------------- 1 | # Migrate code style to Black 2 | 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