https://github.com/phbradley/tcr-dist
Tip revision: c8399203ea24a9270bc7917379ae4504b41c93c7 authored by phbradley on 06 October 2021, 23:19:04 UTC
handle empty clonotype ids in 10x contigs file
handle empty clonotype ids in 10x contigs file
Tip revision: c839920
| File | Mode | Size |
|---|---|---|
| tcrdist | ||
| .gitignore | -rw-r--r-- | 54 bytes |
| DistanceCalculator.py | -rw-r--r-- | 2.5 KB |
| LICENSE.txt | -rw-r--r-- | 1.1 KB |
| README.md | -rw-r--r-- | 6.6 KB |
| all_genes.py | -rw-r--r-- | 10.5 KB |
| amino_acids.py | -rw-r--r-- | 2.2 KB |
| analyze_epitope_privacy.py | -rw-r--r-- | 30.0 KB |
| analyze_gene_frequencies.py | -rw-r--r-- | 9.8 KB |
| analyze_overlap_compute_simpsons.py | -rw-r--r-- | 31.1 KB |
| api.md | -rw-r--r-- | 1.5 KB |
| basic.py | -rw-r--r-- | 4.6 KB |
| blast.py | -rw-r--r-- | 6.3 KB |
| cdr3s_human.py | -rw-r--r-- | 23.9 KB |
| compute_distances.py | -rw-r--r-- | 9.5 KB |
| compute_probs.py | -rw-r--r-- | 10.7 KB |
| create_and_run_testing_datasets.py | -rw-r--r-- | 1.8 KB |
| file_converter.py | -rw-r--r-- | 14.1 KB |
| find_cdr3_motifs.py | -rw-r--r-- | 17.1 KB |
| find_clones.py | -rw-r--r-- | 13.7 KB |
| genetic_code.py | -rw-r--r-- | 4.5 KB |
| html_colors.py | -rw-r--r-- | 8.6 KB |
| logo_tools.py | -rw-r--r-- | 2.8 KB |
| make_10x_clones_file.py | -rw-r--r-- | 19.8 KB |
| make_gene_plots.py | -rw-r--r-- | 50.9 KB |
| make_kpca_plots.py | -rw-r--r-- | 22.5 KB |
| make_mouse_table.py | -rw-r--r-- | 8.5 KB |
| make_really_tall_trees.py | -rw-r--r-- | 28.7 KB |
| make_summary_table.py | -rw-r--r-- | 11.0 KB |
| make_tall_trees.py | -rw-r--r-- | 36.1 KB |
| make_tcr_logo.py | -rw-r--r-- | 16.3 KB |
| parse_cdr3.py | -rw-r--r-- | 5.2 KB |
| parse_tsv.py | -rw-r--r-- | 2.4 KB |
| paths.py | -rw-r--r-- | 875 bytes |
| plot_nbrdist_distributions.py | -rw-r--r-- | 21.0 KB |
| plot_sharing.py | -rw-r--r-- | 21.0 KB |
| random_tcr_distances.py | -rw-r--r-- | 5.2 KB |
| read_motifs.py | -rw-r--r-- | 55.1 KB |
| read_nextgen_matches.py | -rw-r--r-- | 10.5 KB |
| read_pair_seqs.py | -rw-r--r-- | 15.5 KB |
| read_random_tcr_distances.py | -rw-r--r-- | 17.9 KB |
| read_read_nextgen_matches.py | -rw-r--r-- | 29.8 KB |
| read_sanger_data.py | -rw-r--r-- | 19.5 KB |
| rerun_paper_analysis.py | -rw-r--r-- | 2.2 KB |
| run_basic_analysis.py | -rw-r--r-- | 30.0 KB |
| score_trees_devel.py | -rw-r--r-- | 14.2 KB |
| setup.py | -rw-r--r-- | 6.2 KB |
| setup_classic_db.py | -rw-r--r-- | 32.8 KB |
| setup_gammadelta_db.py | -rw-r--r-- | 11.2 KB |
| setup_nextgen_sequence_files.py | -rw-r--r-- | 5.0 KB |
| setup_nextgen_tuple_counts.py | -rw-r--r-- | 4.8 KB |
| svg_basic.py | -rw-r--r-- | 17.0 KB |
| tcr_distances.py | -rw-r--r-- | 12.4 KB |
| tcr_distances_blosum.py | -rw-r--r-- | 7.3 KB |
| tcr_rearrangement.py | -rw-r--r-- | 22.1 KB |
| tcr_rearrangement_new.py | -rw-r--r-- | 9.6 KB |
| tcr_sampler.py | -rw-r--r-- | 38.0 KB |
| translation.py | -rw-r--r-- | 1.5 KB |
| util.py | -rw-r--r-- | 7.6 KB |
