.gitattributes
.gitignore
.gitmodules
LICENSE
README.md
copyright
custom-zenodo.json
example_config.yaml
properdocs.yml
pyproject.toml
.github/workflows/add_remote_files_to_archive.py
.github/workflows/archive.yml
.github/workflows/build_zenodo_archive.sh
.github/workflows/deploy-docs.yml
.github/workflows/git_archive_all_extra.py
.github/workflows/package.yml
.github/workflows/test-install-macos.yml
.github/workflows/test-install-ubuntu.yml
.github/workflows/test-tutorials-macos.yml
.github/workflows/test-tutorials-ubuntu.yml
.github/workflows/zenodo_archive.py
docs/building.md
docs/config.md
docs/formats.md
docs/index.md
docs/requirements.md
docs/testing_installation.md
docs/usage.md
docs/api/README.md
docs/api/visualization.md
docs/images/cytoscape_example.svg
docs/images/density_plot.svg
docs/images/distance_heatmap.svg
docs/images/nj_tree.svg
docs/images/pcoa_2d.svg
docs/images/pcoa_3d.svg
docs/images/ratio_plot.svg
docs/images/sample_plot.svg
docs/images/size_plot.svg
docs/images/trinity_pcoa_2d.svg
docs/images/trinity_pcoa_3d.svg
docs/installation_guides/macos.md
docs/installation_guides/ubuntu.md
docs/javascripts/mathjax.js
docs/stylesheets/style.css
docs/tutorials/export_and_search/README.md
docs/tutorials/export_and_search/images/igv_snapshot.svg
docs/tutorials/nonspades/README.md
docs/tutorials/nonspades/add_tpm.py
docs/tutorials/nonspades/assign_gene_ids.py
docs/tutorials/nonspades/trinity_assembly.md
docs/tutorials/reads2tree/README.md
docs/tutorials/reads2tree/make_heatmap.py
docs/tutorials/reads2tree/make_pcoa.py
docs/tutorials/reads2tree/make_tree.py
docs/tutorials/reads2tree/tall_fescue_accs.csv
docs/tutorials/subsets/README.md
mkdocs_functions/__init__.py
src/rna_clique/__init__.py
src/rna_clique/app.py
src/rna_clique/build_graph.py
src/rna_clique/config.py
src/rna_clique/export_and_search.py
src/rna_clique/export_graph.py
src/rna_clique/export_matrix.py
src/rna_clique/export_orthologs.py
src/rna_clique/filtered_distance.py
src/rna_clique/filtering_step.py
src/rna_clique/find_all_pairs.py
src/rna_clique/find_homologs.py
src/rna_clique/gene_matches_tables.py
src/rna_clique/graph.py
src/rna_clique/identity.py
src/rna_clique/make_subset.py
src/rna_clique/marshalling_dataclass.py
src/rna_clique/metadata.py
src/rna_clique/path_to_sample.py
src/rna_clique/plot_component_sizes.py
src/rna_clique/rna_clique.py
src/rna_clique/search_ideal_components.py
src/rna_clique/select_top_genes.py
src/rna_clique/select_top_genes_all.py
src/rna_clique/similarity_computer.py
src/rna_clique/strand_sat.py
src/rna_clique/sublisted_colormap.py
src/rna_clique/subset_comparisons.py
src/rna_clique/transcripts.py
src/rna_clique/unfiltered_distance.py
src/rna_clique.egg-info/PKG-INFO
src/rna_clique.egg-info/SOURCES.txt
src/rna_clique.egg-info/dependency_links.txt
src/rna_clique.egg-info/entry_points.txt
src/rna_clique.egg-info/requires.txt
src/rna_clique.egg-info/top_level.txt
src/rna_clique/docs/__init__.py
src/rna_clique/docs/docs.py
src/rna_clique/docs/make_config_guide.py
src/rna_clique/docs/make_config_template.py
src/rna_clique/docs/make_usage_guide.py
src/rna_clique/docs/markdown.py
src/rna_clique/viz/__init__.py
src/rna_clique/viz/auto_markers.py
src/rna_clique/viz/confidence_ellipsoid.py
src/rna_clique/viz/heatmap.py
src/rna_clique/viz/pcoa.py
src/rna_clique/viz/phylo_utils.py
src/rna_clique/viz/plots.py
tests/test_install/macos.sh
tests/test_install/ubuntu.sh
tests/test_tutorial/test_export_and_search.sh
tests/test_tutorial/test_nonspades.sh
tests/test_tutorial/test_reads2tree.sh
tests/test_tutorial/test_subsets.sh
tests/verify_install/get_yaml_key.py
tests/verify_install/minimal_config.yaml
tests/verify_install/test_install.sh
tests/verify_install/verify_distances.py