msk_spectrum_tme_2022: CD45 sort-fraction caveat + sort-fraction track - #2342
Draft
inodb wants to merge 2 commits into
Draft
msk_spectrum_tme_2022: CD45 sort-fraction caveat + sort-fraction track#2342inodb wants to merge 2 commits into
inodb wants to merge 2 commits into
Conversation
… profile descriptions The cell-type fraction profiles are derived from CD45 FACS-sorted scRNA-seq, so each sample's composition reflects its sort gate rather than whole-tumor cellularity. Flag this with a 'Caveat:' marker in profile_description so the OncoPrint surfaces it as a per-track warning.
inodb
changed the title
inodb
force-pushed
the
msk-spectrum-cell-sort-caveat
branch
4 times, most recently
from
July 1, 2026 18:56
c6eb326 to
21e65bd
Compare
…_2022 Categorical generic-assay track (generic_assay_type SINGLE_CELL_GATING, stable_id cell_gating) recording which CD45 flow-sort fraction(s) were sequenced per sample (from Vazquez-Garcia et al. 2022, Suppl. Table 2). General type + cell_gating file/stable_id names for cross-study reuse; profile name and values stay CD45-specific. Data file (data_cell_gating.txt) is LFS-tracked, pushed separately.
inodb
force-pushed
the
msk-spectrum-cell-sort-caveat
branch
from
July 1, 2026 19:56
21e65bd to
89472ad
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
What
Two related additions for
msk_spectrum_tme_2022, both about the study's CD45 FACS-sorted single-cell data:Caveat in the cell-type profile descriptions — the relative + absolute cell-type fraction profiles gain a
Caveat:note. These fractions come from CD45-sorted scRNA-seq, so a sample's composition reflects its sort gate (some samples are immune-only or non-immune-only) rather than whole-tumor cellularity. The frontend rendersCaveat:as a ⚠ per-track warning (Surface profile data caveats as a per-track warning in OncoPrint cbioportal-frontend#5637).New
CD45 Sort Fractiongeneric-assay track (SINGLE_CELL_GATING, categorical) — records which CD45 fraction(s) were actually sequenced per sample (CD45-positive (immune)/CD45-negative (non-immune)/CD45-positive and negative/Unknown), derived from the paper's Supplementary Table 2 (aliquot IDs encodeCD45P/CD45N) and matched to sample barcodes via the MSK-IMPACT + Bulk-WGS crosswalks. Keeps all single-cell data under generic assay, and explains the one-sided compositions the caveat warns about.Files
meta_relative_fraction.txt,meta_absolute_counts.txt—Caveat:appended toprofile_descriptionmeta_cell_gating.txt— new categorical generic-assay profile (in this PR)data_cell_gating.txt— the sort-fraction values (LFS — pending push)Companion frontend PR: cBioPortal/cbioportal-frontend#5637
🤖 Generated with Claude Code