.gitattributes
.gitignore
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DESCRIPTION.md
LICENSE
MANIFEST.in
README.md
codecov.yaml
environment.yml
requirements_dev.txt
setup.cfg
setup.py
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bin/blastn
bin/igblastn
bin/makeblastdb
bin/tigger-genotype.R
container/dandelion_preprocess.py
container/environment.yml
container/example_meta.csv
container/sc-dandelion.def
dandelion/__init__.py
dandelion/logging/__init__.py
dandelion/logging/_badge.py
dandelion/logging/_logging.py
dandelion/logging/_metadata.py
dandelion/logging/version.py
dandelion/plotting/__init__.py
dandelion/plotting/_plotting.py
dandelion/preprocessing/__init__.py
dandelion/preprocessing/_preprocessing.py
dandelion/preprocessing/external/__init__.py
dandelion/preprocessing/external/_preprocessing.py
dandelion/tools/__init__.py
dandelion/tools/_diversity.py
dandelion/tools/_network.py
dandelion/tools/_tools.py
dandelion/utilities/__init__.py
dandelion/utilities/_core.py
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docs/modules/dandelion.preprocessing.external.assigngenes_igblast.rst
docs/modules/dandelion.preprocessing.external.creategermlines.rst
docs/modules/dandelion.preprocessing.external.makedb_igblast.rst
docs/modules/dandelion.preprocessing.external.parsedb_heavy.rst
docs/modules/dandelion.preprocessing.external.parsedb_light.rst
docs/modules/dandelion.preprocessing.external.recipe_scanpy_qc.rst
docs/modules/dandelion.preprocessing.external.tigger_genotype.rst
docs/modules/dandelion.preprocessing.filter_bcr.rst
docs/modules/dandelion.preprocessing.format_fasta.rst
docs/modules/dandelion.preprocessing.format_fastas.rst
docs/modules/dandelion.preprocessing.quantify_mutations.rst
docs/modules/dandelion.preprocessing.reannotate_genes.rst
docs/modules/dandelion.preprocessing.reassign_alleles.rst
docs/modules/dandelion.tools.clone_centrality.rst
docs/modules/dandelion.tools.clone_degree.rst
docs/modules/dandelion.tools.clone_diversity.rst
docs/modules/dandelion.tools.clone_overlap.rst
docs/modules/dandelion.tools.clone_rarefaction.rst
docs/modules/dandelion.tools.clone_size.rst
docs/modules/dandelion.tools.define_clones.rst
docs/modules/dandelion.tools.extract_edge_weights.rst
docs/modules/dandelion.tools.find_clones.rst
docs/modules/dandelion.tools.generate_network.rst
docs/modules/dandelion.tools.transfer.rst
docs/modules/dandelion.utilities.Dandelion.rst
docs/modules/dandelion.utilities.concat.rst
docs/modules/dandelion.utilities.from_scirpy.rst
docs/modules/dandelion.utilities.load_data.rst
docs/modules/dandelion.utilities.makeblastdb.rst
docs/modules/dandelion.utilities.read_10x_airr.rst
docs/modules/dandelion.utilities.read_h5.rst
docs/modules/dandelion.utilities.read_pkl.rst
docs/modules/dandelion.utilities.to_scirpy.rst
docs/modules/dandelion.utilities.update_metadata.rst
docs/notebooks/0_dandelion_primer.ipynb
docs/notebooks/1_dandelion_preprocessing-10x_data.ipynb
docs/notebooks/1b_dandelion_noreannotation-10x_data.ipynb
docs/notebooks/1c_dandelion_scirpy.ipynb
docs/notebooks/2_dandelion_filtering-10x_data.ipynb
docs/notebooks/3_dandelion_findingclones-10x_data.ipynb
docs/notebooks/4_dandelion_visualization-10x_data.ipynb
docs/notebooks/5_dandelion_diversity_and_mutation-10x_data.ipynb
docs/notebooks/6_dandelion_running_from_R-10x_data.ipynb
docs/notebooks/7_dandelion_TCR_data_10x_data.ipynb
docs/notebooks/singularity_preprocessing.ipynb
docs/notebooks/img/dandelion_class.png
docs/notebooks/img/dandelion_logo.png
docs/notebooks/img/dandelion_logo_illustration.png
docs/notebooks/img/dandelion_overview.png
sc_dandelion.egg-info/PKG-INFO
sc_dandelion.egg-info/SOURCES.txt
sc_dandelion.egg-info/dependency_links.txt
sc_dandelion.egg-info/not-zip-safe
sc_dandelion.egg-info/requires.txt
sc_dandelion.egg-info/top_level.txt
tests/fixtures.py
tests/r_dependencies.R
tests/r_install.R
tests/test_airr.py
tests/test_importr.py
tests/test_preprocessing.py
tests/test_tools.py
tests/test_tr_preprocessing.py