CIPHER: curated single-cell perturbation datasets — supplement

Supplementary inputs for the CIPHER supplementary analyses (Kuznets-Speck et al., Fluctuation structure predicts genome-wide perturbation outcomes), companion to the main record. Three groups of primary inputs with no other public home: Drug-resistance objects — analysis-ready AnnData for the naive/resistant melanoma and pancreatic comparisons, labelled by obs['Condition']. GEO publishes only the raw GSE233766_RAW.tar; these processed objects come from the authors. LARRY lineage tracing — the stateFate_inVitro_* normalized count matrix, clone matrix, gene names, cell metadata and trajectory/pseudotime tables. Interaction tables — collapsed human genetic-interaction and protein-protein-interaction edge lists used to score CIPHER couplings. Regenerable caches are deliberately excluded — the precomputed_* covariance/forward caches and response-breadth tables are rebuilt from the base objects with the generators in notebooks/src/. Files filesizecontentsmd5Xtot_naive_resistant_melanoma_unbalanced.h5ad4.27 GB16,277 cells x 32,738 genes; 2 Condition levels: Naive, Resistant; control is obs['Condition'] == 'Naive' (8,838 cells); array, int649f4fab2df77c8387414b4c4abe6c92afHuman_genetic_interactions_collapsed.csv1.7 MB18,319 rows x 9 columns; columns: Experimental System, Experimental System Type, Throughput ...ee9dfde76281e01ff9c72e7483bf5292Human_protein_protein_interactions_collapsed.csv93.2 MB973,491 rows x 9 columns; columns: Experimental System, Experimental System Type, Throughput ...21718a6ea9e5fe87f97510af9ec6f537Xtot_four_conditions_balanced.h5ad32.9 MB120 cells x 32,738 genes; 4 Condition levels: Naive, Resistant, Tolerant, Primary; control is obs['Condition'] == 'Naive' (30 cells); array, int64939cb49af688b98f70179f87403493e3Xtot_naive_resistant_unbalanced_resistant_BC50_clone_size_gt1.h5ad3.26 GB12,451 cells x 32,738 genes; 2 Condition levels: Naive, Resistant; control is obs['Condition'] == 'Naive' (9,268 cells); array, int64f3aee1cc0b960b3f4b3ecee3b670fca1pancreatic_naive_vs_resistant.h5ad529.9 MB9,629 cells x 17,685 genes; 2 Condition levels: Naive, Resistant; control is obs['Condition'] == 'Naive' (7,328 cells); csr_matrix, int646f1a562eb034147496de60c1c1da4744stateFate_inVitro_clone_matrix.mtx.gz0.2 MBMatrix Market sparse matrix, 130,887 x 5,864, 49,302 non-zeros (0.01% dense)c64461d36700a67233090664b766f20astateFate_inVitro_gene_names.txt.gz0.1 MB25,289 lines; first line: '0610006L08Rik'dcb3c2d60f0560b52f77782dd2a0d1f9stateFate_inVitro_metadata.txt.gz2.2 MB130,888 lines; first line: 'Library\tCell barcode\tTime point\tStarting population\tCell type annotation\tWell\tSPRING-x\tSPR'a00fa8fb3360d08d4096215b6ec22be8stateFate_inVitro_neutrophil_monocyte_trajectory.txt.gz0.2 MB96,374 lines; first line: 'Cell index'300c42b448fd516780a7f8920c68d53dstateFate_inVitro_neutrophil_pseudotime.txt.gz0.3 MB61,311 lines; first line: 'Cell index\tpseudotime'c17ee4cc0c615a2b30feef17f6394a08stateFate_inVitro_normed_counts.mtx.gz2.07 GBMatrix Market sparse matrix, 130,887 x 25,289, 176,867,560 non-zeros (5.34% dense)eb3cb93097f063f3f6ba5dd2ddbd847f Paths shown relative to CIPHER_DATA_DIR in resources/zenodo_manifest.csv.