Archive 4 checkpoints (1-4)

.gitattributes

@@ -271,3 +271,4 @@ paper-releases/pbisc-diffusion/updates/20261015T100456Z-figure1-diffusion-readab
 paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/NEW_RESULTS_REVIEW.pdf filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/PBISC-Diffusion_expanded_master_20261015_x1_priority.pdf filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/PBISC-Diffusion_expanded_master_20261015_x1_priority.pptx filter=lfs diff=lfs merge=lfs -text
+paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/reference/hgnc_complete_set_downloaded.tsv filter=lfs diff=lfs merge=lfs -text

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/prior_panel_comparison.csv

@@ -0,0 +1,7 @@
+panel,n_genes,overlap_final6k,path,bytes,sha256
+final2k,2000,2000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/2k/selected_genes.csv,148450,4d7d5cfdd56872cf07a211864fc5e6b2aa9f696f650a26add4036e8bafb436a0
+final6k,6000,6000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/selected_genes.csv,451366,09248a3930e3fdefe1dbcd5d60cae4be81028526dcf097dd78169f5a415edfb6
+floor01_15114,15114,6000,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/p15k/selected_genes.csv,1146740,d9def4c24f8a7cea6e41be9e12c814b5ce6927d640cd879131d1047d30a005ef
+legacy2k_32768sample,2000,1998,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/hvg_2000_train256x128_seed20260627/selected_genes.csv,141269,9ced976a4c10675f9628429e010faf3b6befcae9e3cf8336e7a26b942dbc3a3a
+legacy3k_32768sample,3000,2975,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/hvg_3000_train256x128_seed20260627/selected_genes.csv,212756,a0dd75327fd0e22cc445d63eadd17e60dc46ac9a9777dc6e41b887798c12e673
+legacy6k_v3,6000,4258,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_train256x128_seed20260627_v3/tiers/6k/selected_genes.csv,430349,7885e3823bbd9968be03e19d30179bd8ad7558dd63602dbcc7de3a309f08b4c3

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/rare_cohort_targets.csv

@@ -0,0 +1,99 @@
+population_or_program,context,tissue_scope,evidence_roles,source_dois,source_urls,source_scope,rarity_claim,author_fine_label_recovery,core_required_symbols,raw_available_Ensembl_genes,available_6k,available_7k,available_8k
+ASDC_AXL_SIGLEC6,human primary cells,blood,disambiguation; identity,10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,11,81,45,81,81
+ASDC_tDC_activated,human primary cells,blood_in-vitro-viral-stimulation,state,10.1038/s41590-023-01545-7,https://www.nature.com/articles/s41590-023-01545-7,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,1,1,1,1
+ASDC_tDC_cDC2_transition,human primary cells,blood;in-vitro-culture,disambiguation,10.1038/s41590-023-01545-7,https://www.nature.com/articles/s41590-023-01545-7,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,10,8,10,10
+Blood_DN2_atypical_B_reference,Healthy peripheral sorted B-cell subset reference; not SLE-specific disease effect; Healthy sorted peripheral B subsets,blood,disambiguation; identity,10.3389/fimmu.2021.602539,https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.602539/full,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,5,9,9,9,9
+DC3,human primary cells,blood,disambiguation,10.1016/j.immuni.2020.06.002,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,667,362,498,667
+DC3_CD1C_B,human primary cells,blood,disambiguation,10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,55,42,55,55
+DC3_TLR_activated,human primary cells,blood_in-vitro-TLR,state,10.1016/j.immuni.2020.06.002,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,624,309,387,624
+DC3_cDC2,human primary cells,blood,disambiguation; identity,10.1016/j.immuni.2020.06.002,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,8,8,8,8,8
+DC3_cDC2_monocyte_boundary,human primary cells,blood;tissues,disambiguation,10.1016/j.immuni.2019.08.008,https://www.sciencedirect.com/science/article/pii/S1074761319303346,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,6,6,6,6,6
+DC3_monocyte_boundary,human primary cells,blood,disambiguation,10.1016/j.immuni.2020.06.002; 10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/; https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,5,46,32,46,46
+DC4_monocyte_boundary,human primary cells,blood,disambiguation,10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,324,171,277,324
+DRESS_PBMC_perturbed_T_pool,"Refractory SMX/TMP-associated DiHS/DRESS before tofacitinib; blood, not skin/LTT",blood,state,10.1038/s41591-019-0733-7,https://www.nature.com/articles/s41591-019-0733-7,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,5,39,22,39,39
+Furer_BEMP MEBEMP-L/ERYP DEGs,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,8,22,20,22,22
+Furer_BEMP MS4A2 signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,state,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,48,41,48,48
+Furer_BEMP early signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,state,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,21,11,21,21
+Furer_CLP DNTT signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,state,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,12,8,12,12
+Furer_CLP signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,4,36,30,36,36
+Furer_ERYP APOC1 signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,state,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,30,14,30,30
+Furer_ERYP MPP DEGs,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,8,47,21,47,47
+Furer_GMP-L ELANE signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,state,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,35,14,35,35
+Furer_GMP-L signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,16,16,8,16,16
+Furer_MEBEMP-L MHC-II signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,state,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,6,6,6,6,6
+Furer_MKP MEBEMP-L/ERYP DEGs,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,4,63,22,63,63
+Furer_MPP ERYP DEGs,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,34,27,34,34
+Furer_cHSC_vs_immediate_branches,CD34-enriched circulating HSPC; healthy reference across lifespan; used with cytopenia/MDS cases,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,14,12,10,12,12
+Furer_pre-B pro-B DEGs,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,54,33,54,54
+Furer_pre-B signature,Circulating CD34-enriched blood HSPC; healthy reference plus cytopenia/MDS/MDS-MPN; within-state modules separate from abundance,blood,disambiguation,10.1038/s41591-025-03716-5,https://www.nature.com/articles/s41591-025-03716-5,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,4,35,15,35,35
+Giroux_preIgG_CD14_program,Early outpatient mild/moderate COVID-19 pre-IgG seroconversion vs healthy; matched scRNA/scATAC; Early outpatient mild/moderate COVID-19 vs healthy,blood,disambiguation; state,10.1038/s41598-022-15668-8,https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,6,5,6,6
+ILC1_NK_boundary,human primary cells,tonsil;inflamed-intestine,disambiguation,10.1038/ni.2534,https://www.nature.com/articles/ni.2534,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,5,5,5,5
+ILC1_T_NK_boundary,human primary cells,blood;tonsil,disambiguation,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,10,10,10,10,10
+ILC1_T_boundary,human primary cells,blood;tonsil,disambiguation,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,39,28,39,39
+ILC1_tissue,human primary cells,tonsil;inflamed-intestine,identity,10.1038/ni.2534,https://www.nature.com/articles/ni.2534,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,2,2,2,2
+ILC2,human primary cells,blood; blood;tonsil; blood;tonsil;lung,identity; state,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,12,128,63,128,128
+ILC2_activated,human primary cells,lung; lung;in-vitro-alarmin-treated-blood,state,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,14,10,11,14
+ILC2_regulation,human primary cells,blood;tonsil;lung,state,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,27,12,27,27
+ILC3,human primary cells,colon;lung;tonsil; colon;tonsil,identity,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,144,69,86,144
+ILC3_activated,human primary cells,colon;lung; tonsil;gut;in-vitro-cytokine-stimulation,state,10.1016/j.jaci.2017.01.045; 10.1038/s41422-020-00445-x,https://pubmed.ncbi.nlm.nih.gov/28433688/; https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,9,3,7,9
+ILCP_T_B_progenitor_boundary,human primary cells,blood,disambiguation,10.1016/j.cell.2017.02.021,https://www.sciencedirect.com/science/article/pii/S009286741730199X,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,6,4,6,6
+ILCP_naive_ILC,human primary cells,blood,disambiguation; identity,10.1016/j.cell.2017.02.021; 10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x; https://www.sciencedirect.com/science/article/pii/S009286741730199X,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,14,484,266,390,484
+ILCP_vs_mature_ILC,human primary cells,blood,disambiguation,10.1016/j.cell.2017.02.021,https://www.sciencedirect.com/science/article/pii/S009286741730199X,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,11,7,11,11
+Imperial_dexamethasone_associated_monocyte,ESKD COVID-19 Wave 2 (2021); post-glucocorticoid versus pretreatment; absent Wave 1; ESKD COVID-19 Wave 2; dex cluster versus classical/IFN monocytes,blood,disambiguation; state,10.1016/j.xgen.2025.100918,https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,12,12,12,12,12
+Imperial_severe_COVID_monocyte,Severe/critical versus mild/moderate COVID-19 in ESKD,blood,disambiguation; state,10.1016/j.xgen.2025.100918,https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,11,11,11,11
+Influenza_vaccine_effector_memory_B,Blood HA-specific IgD-negative B cells 7-21 days after inactivated influenza vaccination,blood,state,10.1016/j.immuni.2023.03.001,https://pmc.ncbi.nlm.nih.gov/articles/PMC10113805/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,6,5,6,6
+JDM2022_C1Q_mono_disambiguation,JDM inflammatory CD16 vs inflammatory CD14 monocyte subclusters,blood,disambiguation,10.3389/fimmu.2022.902232,https://pmc.ncbi.nlm.nih.gov/articles/PMC9254730/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,3,3,3,3,3
+JDM2022_CD14inflam CM v CD14 CM,Treatment-naive JDM PBMC and 2/4/6 month post-treatment; 4 longitudinal TN-JDM plus 4 inactive JDM,blood,state,10.3389/fimmu.2022.902232,https://pmc.ncbi.nlm.nih.gov/articles/PMC9254730/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,39,36,39,39
+JDM2022_CD16+inflam nCM v CD16+ nCM,Treatment-naive JDM PBMC and 2/4/6 month post-treatment; 4 longitudinal TN-JDM plus 4 inactive JDM,blood,state,10.3389/fimmu.2022.902232,https://pmc.ncbi.nlm.nih.gov/articles/PMC9254730/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,1,39,35,39,39
+JDM2022_CD16inflam nCM v CD14inflam CM,Treatment-naive JDM PBMC and 2/4/6 month post-treatment; 4 longitudinal TN-JDM plus 4 inactive JDM,blood,state,10.3389/fimmu.2022.902232,https://pmc.ncbi.nlm.nih.gov/articles/PMC9254730/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,6,40,21,40,40
+JDM_activated_IFN_monocyte,Treatment-naive JDM vs healthy controls,blood,state,10.1172/jci.insight.176963,https://pmc.ncbi.nlm.nih.gov/articles/PMC11383589/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,3,3,1,3,3
+JDM_activated_effector_Treg,JDM disease-activity associated peripheral Tregs,blood,state,10.1172/jci.insight.176963,https://pmc.ncbi.nlm.nih.gov/articles/PMC11383589/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,7,7,7,7,7
+JDM_immature_B_B9,Treatment-naive active JDM and follow-up/inactive blood; 15 patients 22 samples plus 5 controls,blood,identity,10.1172/jci.insight.176963,https://pmc.ncbi.nlm.nih.gov/articles/PMC11383589/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,3,3,3,3,3
+JDM_proliferative_NK_NK12,JDM disease activity validation cohort,blood,state,10.1172/jci.insight.176963,https://pmc.ncbi.nlm.nih.gov/articles/PMC11383589/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,2,2,2,2,2
+Ji_ChILI_PBMC_program,TOL vs BC/AC in ICI-associated liver injury,blood,state,10.1007/s00262-025-04033-z,https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,1,1,1,1,1
+Ji_ChILI_bulk_PBMC_program,ChILI time of liver injury vs ICI-treated no injury and pre-ICI baseline,blood,state,10.1007/s00262-025-04033-z,https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,24,17,24,24
+NK_ILC1_boundary,human primary cells,blood;tonsil;lung;colon,disambiguation,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,108,94,108,108
+RA_CD4_IFIT_activated_T,RA peripheral CD4 IFIT subset vs other CD4 subsets,blood,state,10.1172/jci.insight.178499,https://pmc.ncbi.nlm.nih.gov/articles/PMC11343607/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,5,5,4,5,5
+RA_IFITM3_IFN_monocyte,RA blood; 18 RA and 18 matched controls; mixed treatments,blood,state,10.1172/jci.insight.178499,https://pmc.ncbi.nlm.nih.gov/articles/PMC11343607/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,3,3,3,3,3
+RA_gdT_disease_state,RA vs matched controls within gamma-delta T,blood,state,10.1172/jci.insight.178499,https://pmc.ncbi.nlm.nih.gov/articles/PMC11343607/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,6,6,6,6
+Reyes_MS1B_proresolving_module,Human bacterial sepsis,blood,state,10.1038/s41591-020-0752-4,https://pmc.ncbi.nlm.nih.gov/articles/PMC7235950/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,4,3,4,4
+Reyes_MS1_sepsis_monocyte,"Sepsis vs non-septic infection/sterile critical illness; primary UTI samples within 12h ED, secondary cohorts >=24h",blood,state,10.1038/s41591-020-0752-4,https://pmc.ncbi.nlm.nih.gov/articles/PMC7235950/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,3,3,3,3,3
+Reyes_MS1_sepsis_specific_subprogram,ICU-SEP vs ICU-NoSEP within MS1,blood,state,10.1038/s41591-020-0752-4,https://pmc.ncbi.nlm.nih.gov/articles/PMC7235950/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,2,2,2,2,2
+SLE_DN2_effector_B,Active SLE and nephritis; blood B cells vs DN1/naive/switched memory; SLE DN2 vs other B subsets,blood,disambiguation; identity,10.1016/j.immuni.2018.08.015,https://pmc.ncbi.nlm.nih.gov/articles/PMC6217820/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,11,10,8,10,10
+SLE_immature_CD10neg_LDG,SLE CD10-negative vs CD10-positive LDG and normal-density neutrophils; SLE peripheral low-density granulocytes; subset comparison,blood,disambiguation; state,10.1073/pnas.1908576116,https://pmc.ncbi.nlm.nih.gov/articles/PMC6911190/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,10,10,7,10,10
+Ye_B_c05-AIM2,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,33,21,33,33
+Ye_B_c06-AIM2-CD27,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,33,25,33,33
+Ye_B_c07-MZB1,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,identity,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,54,21,54,54
+Ye_B_c08-MKI67,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,34,9,34,34
+Ye_CD4_NR4A2_central_memory,Adult and pediatric sepsis source contrasts,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,2,2,2,2,2
+Ye_CD8_GNLY_CCL4hi,Adult abdominal/pulmonary sepsis versus other source groups and controls,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,4,4,4,4,4
+Ye_HSC,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,identity,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,59,46,59,59
+Ye_Macrophage,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,42,13,42,42
+Ye_Megakaryocyte,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,identity,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,60,46,60,60
+Ye_Mono-c03-CD14-RETN,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,48,20,48,48
+Ye_Mono-c06-CD14-MKI67,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,80,53,80,80
+Ye_Mono_c06_CD14_MKI67_pediatric,Pediatric pulmonary sepsis enrichment; abdominal sepsis/HC/ICU controls; Pediatric sepsis source contrasts,blood,disambiguation; state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,8,8,8,8,8
+Ye_NKT_IFNG_CCL4hi,Adult abdominal/pulmonary sepsis versus other source groups and controls,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,4,4,4,4,4
+Ye_NKT_c05-IFNG-CCL4,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,48,45,48,48
+Ye_NK_PRF1_CCL4hi,Adult abdominal/pulmonary sepsis versus other source groups and controls,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,4,4,4,4,4
+Ye_NK_c03-PRF1-CCL4,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,47,45,47,47
+Ye_NK_c04-MKI67,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,35,25,35,35
+Ye_T_CD4_c02-GPR183-NR4A2,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,57,31,57,57
+Ye_T_CD4_c06-FOXP3,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,identity,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,37,31,37,37
+Ye_T_CD4_c07-MKI67,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,35,17,35,35
+Ye_T_CD8_c05-GNLY-CCL4,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,48,39,48,48
+Ye_T_CD8_c06-MKI67,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,state,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,35,22,35,35
+Ye_T_CD8_c07-TRAV1-2,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,identity,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,45,35,45,45
+Ye_gdT,Sepsis discovery PBMC pooled subset-versus-rest marker analysis; exact disease contrast not equivalent to differential abundance,blood,identity,10.1038/s41590-025-02345-x,https://www.nature.com/articles/s41590-025-02345-x,same_benchmark_source_endpoint_informed,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,47,47,47,47
+cDC1,human primary cells,blood; lung;NSCLC,identity,10.1038/s41586-020-2134-y; 10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/; https://www.nature.com/articles/s41586-020-2134-y,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,3,382,205,272,355
+cDC2,human primary cells,blood; lung;NSCLC,disambiguation; identity,10.1016/j.immuni.2020.06.002; 10.1038/s41586-020-2134-y; 10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/; https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/; https://www.nature.com/articles/s41586-020-2134-y,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,837,508,650,773
+cDC2_DC3_boundary,human primary cells,blood,disambiguation,10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,42,31,42,42
+cDC2_TLR_activated,human primary cells,blood_in-vitro-TLR,state,10.1016/j.immuni.2020.06.002,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,261,162,184,261
+circulating_ILC,human primary cells,blood;tonsil,state,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,10,9,10,10
+monocyte,human primary cells,blood,disambiguation,10.1016/j.immuni.2020.06.002,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,302,158,261,302
+monocyte_TLR_activated,human primary cells,blood_in-vitro-TLR,state,10.1016/j.immuni.2020.06.002,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,568,302,380,568
+monocyte_vs_DC3,human primary cells,blood,disambiguation,10.1016/j.immuni.2020.06.002,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,3,3,3,3,3
+mregDC_state,human primary cells,lung;NSCLC,state,10.1038/s41586-020-2134-y,https://www.nature.com/articles/s41586-020-2134-y,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,272,153,181,272
+pDC,human primary cells,blood,identity,10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,11,331,192,293,331
+pDC_ASDC_cDC_boundary,human primary cells,blood,disambiguation,10.1126/science.aah4573,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,15,15,13,15,15
+tissue_ILC_activation,human primary cells,colon;lung;tonsil,state,10.1038/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,external_reference_exposure_not_fully_audited,not established by marker list; requires specimen/donor-level prevalence,not established by panel membership or generic marker co-detection,0,1,1,1,1

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/rare_sampling_sensitivity.csv

@@ -0,0 +1,7 @@
+N_generated,assumed_prevalence,expected_ILC,prob_zero_iid,assumption
+150,0.000496026417729135,0.07440396265937026,0.9282794853971987,hypothetical IID exact source-label prevalence; not observed generation
+256,0.000496026417729135,0.12698276293865857,0.8807211074713666,hypothetical IID exact source-label prevalence; not observed generation
+1000,0.000496026417729135,0.496026417729135,0.6088706205766332,hypothetical IID exact source-label prevalence; not observed generation
+1500,0.000496026417729135,0.7440396265937025,0.4751027325434979,hypothetical IID exact source-label prevalence; not observed generation
+4000,0.000496026417729135,1.98410567091654,0.13743586347974582,hypothetical IID exact source-label prevalence; not observed generation
+6038,0.000496026417729135,2.9950075102485174,0.049999085816253376,hypothetical IID exact source-label prevalence; not observed generation

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/reference/hgnc_complete_set_downloaded.tsv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2828618d23d315be76ea415f7ef0e951858716ebab07e2d584190f52e5178c1e
+size 16982276