datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
jinyang-omentum-pds-nmf-subtypes-results-v1
jinyang-omentum-pds-nmf-subtypes-results-v1
NMF splicing-subtype clustering + survival analysis on the PDS-only
(Treatment_strategy=='PDS') subset of the Omental-site HGSOC cohort (106 of 168
samples), reusing the exact method from
/Users/depin/src/tries/2026-01-27-three_sites_analysis_from_ovarian_cancer_data_by_cursor_agent.
Tests whether that project's original whole-cohort Omental finding (k=2, log-rank
p=0.0002, HR=2.10, C-index=0.591, n=168 PDS+NACT mixed) is robust to… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-pds-nmf-subtypes-results-v1.jinyang-omentum-rmats-outlier-fixed-biology-results-v1
jinyang-omentum-rmats-outlier-fixed-biology-results-v1
Biology of the k=2 subgroups from jinyang-omentum-rmats-outlier-fixed-clustering (cluster1 n=116 / cluster2 n=50, 166 outlier-excluded omentum samples; expression analyses on the 160-sample TPM-labeled intersection). CAVEAT (stated plainly, not buried): cluster1/cluster2 are collinear with sequencing platform to within one sample -- cluster 2 contains ZERO NovaSeq-6000 samples and cluster 1 is 113/116 NovaSeq-6000. The… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-rmats-outlier-fixed-biology-results-v1.jinyang-gse138866-rseqc-metrics-v1
jinyang-gse138866-rseqc-metrics-v1
FINAL (130/130) per-sample QC table for GSE138866 FFPE omental metastatic HGSOC bulk RNA-seq, complete production run. Pipeline: STAR 2-pass alignment (split pass1/pass2 sbatch steps, GRCh38 Ensembl-113) -> samtools markdup -> RustQC rna (all QC modules in one BAM pass) -> per-sample JSON -> this aggregate table. Both Stage A (STAR alignment, job 75309971) and Stage B (markdup+RustQC, job 75317062) reached 130/130 real completions with ZERO… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse138866-rseqc-metrics-v1.jinyang-gse138866-nmf-subtypes-results-v1
jinyang-gse138866-nmf-subtypes-results-v1
Canary run (N=110 real GSE138866 samples, turso job 75350352, gpu partition/dgx1-01,
completed 2026-09-15T09:04:36Z in ~1m40s) for outcome-blind NMF splicing-subtype
discovery -- a replication attempt of
2026-01-27-three_sites_analysis_from_ovarian_cancer_data_by_cursor_agent's Omental-site
finding (log-rank p=0.0002, C-index=0.591), using the same 10,019 high-confidence AS/PSI
events x 110 samples matrix as the sibling experiment… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse138866-nmf-subtypes-results-v1.lsec-fcn2-splicing-viz-percell-counts-v1
lsec-fcn2-splicing-viz-percell-counts-v1
Per-cell read-level junction counts for the FCN2 SE event, from lsec_bams_dedup (UMI-dedup) split by CB in cell_barcode.tsv.gz. E/I = read counts of the exclusion / inclusion junctions; I = max(inclA, inclB); PSI = I/(I+E). Read-level, NOT UMI-collapsed. Complete 17-sample set from the scale-up re-split (3 canary + 14 added samples), the same rows the full 4-group bampheno consumed.
Dataset Info
Rows: 989
Columns: 8… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/lsec-fcn2-splicing-viz-percell-counts-v1.jinyang-omentum-pds-subtype-biology-results-v1
jinyang-omentum-pds-subtype-biology-results-v1
Whole-cohort Omental k=2 NMF subtype biology (S1 n=118 / S2 n=50, 168 samples; expression analyses on the 162-sample TPM-labeled intersection). Figures: survival-anchor KM, splicing/expression volcanos, ORA dot plots (6), ssGSEA splicing heatmap, per-gene splicing-vs-expression concordance scatter.
Dataset Info
Rows: 11
Columns: 2
Columns
Column
Type
Description
figure_name
Value('string')… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-pds-subtype-biology-results-v1.jinyang-gse138866-splicing-subtypes-results-v1
jinyang-gse138866-splicing-subtypes-results-v1
Canary run (N=110 real GSE138866 samples) for AS-based consensus-clustering molecular
subtype discovery. Outcome: GATE_FAILURE (null result). Only 2/10,019 high-confidence
AS events clear BH-FDR<0.05 (need >=20 to proceed to clustering) -- a pre-specified valid
stopping point ("insufficient power to detect stable AS-based subtypes"), not a pipeline bug.
Downstream clustering/KM/permutation-null artifacts were not produced, per… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse138866-splicing-subtypes-results-v1.lsec-fcn2-splicing-viz-pseudobulk-psi-v1
lsec-fcn2-splicing-viz-pseudobulk-psi-v1
JAseC-faithful pseudobulk PSI replication for the FCN2 SE event, all 17 samples. E/I computed with JAseC's exact counting rules (bamJuncCount_10x: mapped, N-containing CIGAR, CB+UB tags, NH==1, no secondary/supplementary filter, UMI collapse per (junction,strand,cell), antisense merge at same jc_pos). match column compares E_ref/I_ref from the JAseC reference run: 17/17 exact.
Dataset Info
Rows: 17
Columns: 17… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/lsec-fcn2-splicing-viz-pseudobulk-psi-v1.jinyang-omentum-pds-consensus-clustering-results-v1
jinyang-omentum-pds-consensus-clustering-results-v1
Null-result fallback report for the jinyang-omentum-pds-consensus-clustering canary (N=106 PDS-only real data run). Real (unpermuted) pipeline hit the pre-specified '<20 BH-FDR candidates' stopping gate (5 candidates found) -- a valid, reportable outcome, not a pipeline bug. Per design, clustering/KM/permutation-null artifacts were not produced in this branch. This is effectively the TERMINAL result for the real-data question:… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-pds-consensus-clustering-results-v1.jinyang-omentum-novaseq-clustering-results-v1
jinyang-omentum-novaseq-clustering-results-v1
Null-result fallback report for the jinyang-omentum-novaseq-clustering canary (N=115 NovaSeq-6000-only real data run). Real (unpermuted) pipeline hit the pre-specified stopping gate (lt20_candidates) -- a valid, reportable outcome, not a pipeline bug, matching the prior-art precedent's null finding on a different quantification. Independent triangulation via a second, independently-implemented pipeline reaches the same conclusion: no… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-novaseq-clustering-results-v1.jinyang-gse138866-rmats-psi-canary-v1
jinyang-gse138866-rmats-psi-canary-v1
Canary per-sample rMATS-turbo PSI matrix (single-group, --statoff) for 2 GSE138866 samples (GSM4120625, GSM4120690 -- same 2 GSMs used as the jinyang-gse138866-rseqc canary). 158620 events x 2 samples.
Dataset Info
Rows: 158620
Columns: 9
Columns
Column
Type
Description
event_id
Value('large_string')
rMATS event type + numeric ID, e.g. 'SE_4038' (unique within this table -- use this, not 'coords'… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse138866-rmats-psi-canary-v1.lsec-lonp2-splicing-viz-percell-counts-v1
lsec-lonp2-splicing-viz-percell-counts-v1
Per-cell read-level junction counts for the LONP2 SE event, HC vs F2-3 (10 samples), from lsec_bams_dedup (UMI-dedup) split by CB in cell_barcode.tsv.gz. E/I = read counts of the exclusion / inclusion junctions; I = max(inclA, inclB); PSI = I/(I+E). Read-level, NOT UMI-collapsed. Known-null locus — expect PSI=1.00 for nearly all cells in both groups.
Dataset Info
Rows: 38
Columns: 8
Columns
Column… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/lsec-lonp2-splicing-viz-percell-counts-v1.jinyang-gse138866-rmats-psi-matrix-jc-v1
jinyang-gse138866-rmats-psi-matrix-jc-v1
Per-sample rMATS-turbo PSI matrix (JC junction counts), SINGLE-GROUP mode (--b1 only, no --b2, --statoff), for all 130 GSE138866 FFPE omental metastatic HGSOC bulk paired-end RNA-seq samples. NO differential analysis, NO statistical testing -- per-sample PSI only, per explicit user request. Reuses the STAR-aligned BAMs already produced by jinyang-gse138866-rseqc (GRCh38 Ensembl 113) -- no realignment. 227342 events x 130 samples. PSI… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse138866-rmats-psi-matrix-jc-v1.jinyang-omentum-rmats-outlier-fixed-clustering-results-v1
jinyang-omentum-rmats-outlier-fixed-clustering-results-v1
Patient-level permutation-null control, N=50 (canary; final extends to N=200). IMPORTANT CAVEAT (see 01_pipeline.R header and EXPERIMENT_README.md): this tests circularity in the CLUSTERING+LOG-RANK steps ONLY -- the 651 candidate events are FIXED across every permutation draw (they were externally selected using the TRUE survival outcome, not re-derived by this pipeline), so this control does NOT correct for… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-rmats-outlier-fixed-clustering-results-v1.jinyang-omentum-novaseq-p001-clustering-results-v1
jinyang-omentum-novaseq-p001-clustering-results-v1
Null-result fallback report for the jinyang-omentum-novaseq-p001-clustering canary (N=115 NovaSeq-6000-only real data run, published-method raw p<0.001 gate). Real (unpermuted) pipeline hit the pre-specified stopping gate (no_stable_k) -- a valid, reportable outcome, not a pipeline bug.
Dataset Info
Rows: 1
Columns: 12
Columns
Column
Type
Description
outcome
Value('large_string')… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-novaseq-p001-clustering-results-v1.jinyang-omentum-subtype-artifact-mechanism-canary-expression-matrix-v1
jinyang-omentum-subtype-artifact-mechanism-canary-expression-matrix-v1
Canary QC artifact for the expression arm of jinyang-omentum-subtype-artifact-mechanism.
Shiba v0.8.2 expression matrices for 40 canary samples (20 NovaSeq / 20 non-NovaSeq)
over 78,724 genes, from STAR 2nd-pass BAMs against the Ensembl 113 annotation.
This is canary-scale QC data, not a result. 40 of the cohort's 160 samples,
on a 78,724-gene matrix. It exists to prove the pipeline runs, to measure what it… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-subtype-artifact-mechanism-canary-expression-matrix-v1.jinyang-gse138866-rseqc-canary-v1
jinyang-gse138866-rseqc-canary-v1
CANARY (2 of 130) per-sample QC table for GSE138866 FFPE omental metastatic HGSOC bulk RNA-seq. Pipeline: STAR 2-pass alignment (split into pass1-only + pass2-with-on-the-fly-junction-insertion sbatch steps, GRCh38 Ensembl-113) -> samtools markdup -> RustQC rna (all QC modules in one BAM pass) -> per-sample JSON -> this aggregate table. Validates the full pipeline E2E (including the Stage A pass1/pass2 split and a Stage B markdup OOM fix… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse138866-rseqc-canary-v1.lsec-sicilian-lonp2-pilot-results-v1
lsec-sicilian-lonp2-pilot-results-v1
Pilot results (5 samples) from re-detecting splice junctions with SICILIAN
(Dehghannasiri, Olivieri, Salzman -- Genome Biology 2021) on raw FASTQ, to test whether the
LONP2 skipped-exon (SE) event's null result (3x via STARsolo -> JAseC/SHIBA) is a methods
artifact. See experiment lsec-sicilian-lonp2 for the full design, red-team review, and
debugging history.
The LONP2 SE event (hg38)
5' constitutive exon:… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/lsec-sicilian-lonp2-pilot-results-v1.jinyang-omentum-subtype-artifact-mechanism-canary-splice-enrichment-v1
jinyang-omentum-subtype-artifact-mechanism -- canary splicing-arm, enrichment summary
One row per rMATS event type. Every value is read directly out of the job's own
splicing_gates.json; nothing here is retyped by hand.
Read this before quoting any number
None of the enrichment results below is a scientific finding. This is a
canary: chr21+chr22 only, 40 of 1048 samples. Its job was to prove the
enrichment code path runs and emits a well-formed null. It did. The… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-subtype-artifact-mechanism-canary-splice-enrichment-v1.jinyang-omentum-subtype-artifact-mechanism-canary-strandedness-control-v1
omentum-subtype-artifact-mechanism -- canary strandedness control
Answers one question before any TPM is trusted: is the pinned featureCounts
strandedness (-s 2) correct for this cohort?
experiment.yaml pins stranded counting. Upstream Shiba passes no -s at all,
i.e. unstranded, so this is the one deliberate local deviation from upstream,
and the run is only interpretable if the deviation is right. Nothing in the
project had ever measured it, so the canary did.… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-subtype-artifact-mechanism-canary-strandedness-control-v1.jinyang-omentum-subtype-artifact-mechanism-canary-splice-events-v1
jinyang-omentum-subtype-artifact-mechanism -- canary splicing-arm, every event
The complete per-event output of the canary differential test: all
38,750 alternative-splicing events on chr21+chr22 across 40 canary
samples, all five rMATS event types. Nothing is filtered out of this table --
events that failed the missingness filter are present with keep=False and
empty p/q, so the exclusions are auditable rather than invisible.
What this is
A CANARY. 40 samples… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-subtype-artifact-mechanism-canary-splice-events-v1.jinyang-omentum-subtype-artifact-mechanism-canary-expression-arm-test-v1
jinyang-omentum-subtype-artifact-mechanism-canary-expression-arm-test-v1
Per-gene differential expression between the two canary arms (20 NovaSeq vs 20
non-NovaSeq), from the TPM matrix in jinyang-omentum-subtype-artifact-mechanism-canary-expression-matrix-v1.
78,724 genes, Mann-Whitney U (two-sided, asymptotic), BH-FDR adjusted.
Read the composition warning before using any gene from this table. The arm
contrast is not a clean platform contrast — see below.
Headline… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-omentum-subtype-artifact-mechanism-canary-expression-arm-test-v1.jinyang-gse186145-mussel-vs-shiba-v1
jinyang-gse186145-mussel-vs-shiba-v1
MUSSEL vs Shiba PSI concordance for GSE186145 — 237k matched events via direct pos_id matching (98.4% of MUSSEL events).
Dataset Info
Rows: 236888
Columns: 105
Columns
Column
Type
Description
pos_id
Value('large_string')
Splicing event position ID (Ensembl convention)
mussel_event_id
Value('large_string')
MUSSEL event identifier (gene-based)
shiba_event_id
Value('large_string')
Shiba event… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse186145-mussel-vs-shiba-v1.jinyang-gse158739-mussel-vs-shiba-v1
jinyang-gse158739-mussel-vs-shiba-v1
MUSSEL vs Shiba PSI concordance for GSE158739 — 207,612 matched events via direct pos_id matching (99.7% of MUSSEL events). Columns: mussel_/shiba_/delta_ per sample, mean_delta, median_delta, max_abs_delta, concordant_samples.
Dataset Info
Rows: 207612
Columns: 45
Columns
Column
Type
Description
pos_id
Value('large_string')
Splicing event position ID (Ensembl convention, e.g.… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse158739-mussel-vs-shiba-v1.