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msk_spectrum_tme_2022: CD45 sort-fraction caveat + sort-fraction track #2342

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msk_spectrum_tme_2022: CD45 sort-fraction caveat + sort-fraction track #2342

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efb4aab
msk_spectrum_tme_2022: note CD45 cell-sorting caveat in generic-assay…
miccheck12 Jun 30, 2026
89472ad
Add scRNA cell_gating generic-assay profile meta for msk_spectrum_tme…
miccheck12 Jul 1, 2026
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2 changes: 1 addition & 1 deletion public/msk_spectrum_tme_2022/meta_absolute_counts.txt
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Expand Up @@ -4,7 +4,7 @@ generic_assay_type: SINGLE_CELL_ABSOLUTE_CELL_TYPE_COUNTS
datatype: LIMIT-VALUE
stable_id: cell_type_absolute_counts
profile_name: Cell Type Absolute Counts
profile_description: Cell Type Absolute Counts
profile_description: Cell Type Absolute Counts. Caveat: Counts are derived from CD45 FACS-sorted scRNA-seq, so each sample's composition reflects its sort gate (some samples are immune-only or non-immune-only) rather than whole-tumor cellularity.
data_filename: data_absolute_counts.txt
show_profile_in_analysis_tab: true
pivot_threshold_value: 0.000001
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10 changes: 10 additions & 0 deletions public/msk_spectrum_tme_2022/meta_cell_gating.txt
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@@ -0,0 +1,10 @@
cancer_study_identifier: msk_spectrum_tme_2022
genetic_alteration_type: GENERIC_ASSAY
generic_assay_type: SINGLE_CELL_GATING
datatype: CATEGORICAL
stable_id: cell_gating
profile_name: scRNA Cell Gating
profile_description: CD45 flow-sort gate(s) sequenced by scRNA-seq for each sample's tumor site (Vazquez-Garcia et al. 2022, Suppl. Table 2). Indicates which compartment(s) the cell-type fraction tracks represent; samples from a single gate show a one-sided (immune-only or non-immune-only) composition rather than whole-tumor cellularity.
data_filename: data_cell_gating.txt
show_profile_in_analysis_tab: true
generic_entity_meta_properties: NAME,DESCRIPTION,URL
2 changes: 1 addition & 1 deletion public/msk_spectrum_tme_2022/meta_relative_fraction.txt
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Expand Up @@ -4,7 +4,7 @@ generic_assay_type: SINGLE_CELL_RELATIVE_CELL_TYPE_COUNTS
datatype: LIMIT-VALUE
stable_id: cell_type_relative_counts
profile_name: Cell Type Relative Fractions
profile_description: Cell Type Relative Fractions.
profile_description: Cell Type Relative Fractions. Caveat: Fractions are derived from CD45 FACS-sorted scRNA-seq, so each sample's composition reflects its sort gate (some samples are immune-only or non-immune-only) rather than whole-tumor cellularity.
data_filename: data_relative_fraction.txt
show_profile_in_analysis_tab: true
pivot_threshold_value: 0.000001
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