diff --git a/public/msk_spectrum_tme_2022/meta_absolute_counts.txt b/public/msk_spectrum_tme_2022/meta_absolute_counts.txt index ac49f8708d..00aaa17fe4 100644 --- a/public/msk_spectrum_tme_2022/meta_absolute_counts.txt +++ b/public/msk_spectrum_tme_2022/meta_absolute_counts.txt @@ -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 diff --git a/public/msk_spectrum_tme_2022/meta_cell_gating.txt b/public/msk_spectrum_tme_2022/meta_cell_gating.txt new file mode 100644 index 0000000000..d4ba5d4c44 --- /dev/null +++ b/public/msk_spectrum_tme_2022/meta_cell_gating.txt @@ -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 \ No newline at end of file diff --git a/public/msk_spectrum_tme_2022/meta_relative_fraction.txt b/public/msk_spectrum_tme_2022/meta_relative_fraction.txt index fe2392e208..d273ef5779 100644 --- a/public/msk_spectrum_tme_2022/meta_relative_fraction.txt +++ b/public/msk_spectrum_tme_2022/meta_relative_fraction.txt @@ -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