luca
Single-cell Lung Cancer Atlas with 1.2M cells
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Download Latest Version (.zip)- .gitignore
- make_h5ad_batch1.py
- make_h5ad_batch2.py
- annotate_lambrechts_2018_luad_6653.py
- annotate_maynard_bivona_2020_nsclc.py
- 21_merge_all.py
- 25_merge_solo.py
- 31_annotate_cell_types_coarse.py
- 32_annotate_cell_types_fine.py
- 33_epithelial_cells.py
- 35_export_atlas.py
- 36_scvi_mapping.py
- 36b_update_annotation.py
- 37_neutrophil_subclustering.py
- 38_patient_stratification.py
- 41_prepare_de_analysis.py
- 51_scissor_analysis.py
- 52_validate_deconvolution.Rmd
- _prepare_scissor_data.Rmd
- 81_export_atlas.py
- .gitignore
- 91_compare_groups.py
- 92_compare_groups_plots.py
- 93_patient_stratification_figures.py
- 94a_cell_type_markers_core_atlas.py
- 94b_overview_plots_core_atlas.py
- 94c_overview_plots_extended_atlas.py
- 94d_cell_type_signatures.py
- 95_compare_platforms.py
- 96a_neutrophils.py
- 96b_neutrophils_velocyto.py
- 97_response_to_icb.Rmd
- 98a_cell_type_composition_luad_lusc.py
- 99_cpdb_analysis.py
- 99b_cpdb_circosplot.Rmd
- _tumor_cell_markers.py
- .gitignore
- integrate_scanvi.py
- integrate_scvi.py
- run_deseq2.R
- scissor_single_sample.R
- build_atlas.config
- downstream_analyses.config
- __init__.py
- cytosig_signature_matrix.tsv
- lung_markers.csv
- __init__.py
- compute_scores.py
- lm.py
- pl.py
- __init__.py
- fixtures.py
- test_integration.py
- test_pseudobulk.py
- __init__.py
- annotation.py
- cell2cell.py
- colors.py
- deconvolution.py
- diversity.py
- integration.py
- pairwise.py
- pseudobulk.py
- signatures.py
- util.py
- .gitignore
- pyproject.toml
- README.rst
- .gitignore
- main.nf
- meta.yml
- parametrize.nf
- main.nf
- meta.yml
- parametrize.nf
- main.nf
- main.nf
- .jupytext
- main.nf
- nxfvars.nf
- qc_plots.py
- scqc-notebook.py
- main.nf
- main.nf
- main.nf
- check_samplesheet.nf
- scissor.nf
- nf_velocyto.config
- README.md
- run_velocyto.sh
- velocyto.nf
- add_additional_datasets.nf
- annotate_dataset.nf
- de_analysis.nf
- integrate_datasets.nf
- neighbors_leiden_umap.nf
- plots_and_comparisons.nf
- scissor.nf
- cell_metadata_maynard.csv.gz
- patient_metadata_corrected.xlsx
- sequencing_platforms.csv
- wu_et_al_additional_patient_metadata.xlsx
- BD_CLS1.txt
- BD_CLS2.txt
- BD_CLS3.txt
- b_cell_signatures.csv
- genecards_growth_factors.csv
- hlca_cell_type_signatures.csv
- immune_checkpoints.csv
- merad_lcam.xlsx
- net_signatures.csv
- neutro_phenotype_genesets.xlsx
- neutro_recruitment_chemokines.xlsx
- pmn_mdsc.csv
- wu_cd8_t_cell_signatures.csv
- braf_mutated.tsv
- clinical_data_for_scissor.tsv
- egfr_mutated.tsv
- kras_mutated.tsv
- mmc1.xlsx
- stk11_mutated.tsv
- tcga_treatment.tsv
- tp53_mutated.tsv
- cellphonedb_2022-04-06.tsv
- gene_symbol_dict.csv
- patient_table_batch1_3_patients.xlsx
- patient_table_batch2.xlsx
- patient_table_orig.xlsx
- samplesheet_scrnaseq_preprocessing.csv
- samplesheet_scrnaseq_preprocessing2.csv
- study_dois.csv
- symbol_to_ensembl.csv
- adata_all_celltypes.h5ad
- .gitignore
- main.nf
- build_atlas.nf
- downstream_analyses.nf
- .editorconfig
- .env
- .gitattributes
- .gitignore
- LICENSE
- main.nf
- nextflow.config
- pack_for_zenodo.sh
- README.md
- run_build_atlas.sh
- run_downstream_analyses.sh
# Installation Guide
1. Get the code
git clone https://github.com/icbi-lab/luca
Downloads the entire project code from GitHub to your computer.
cd luca
Moves into the project folder you just downloaded.
2. Python
Easy RecommendedPrerequisites
โ ๏ธ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.
pip install .
Installs the package published on PyPI directly โ no need to clone the source.
python <์คํํ ํ์ผ๋ช
>.py # README์์ ์ ํํ ์คํ ํ์ผ๋ช
์ ํ์ธํ์ธ์
Runs the Python script (or module).
If it runs without errors and prints output in the terminal, it worked.
// repository documentation
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