Datasetpublic

depinwang/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.

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Dataset Card

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 (bamJuncCount10x: mapped, N-containing CIGAR, CB+UB tags, NH==1, no secondary/supplementary filter, UMI collapse per (junction,strand,cell), antisense merge at same jcpos). match column compares Eref/Iref from the JAseC reference run: 17/17 exact.

Dataset Info

—Rows: 17
—Columns: 17

Columns

Column	Type	Description
srr	Value('large_string')	sample (SRA run id)
group	Value('large_string')	Healthy / F0 / F2-3 / F4
E	Value('int64')	UMI-collapsed exclusion-junction counts (both strands merged)
inclA	Value('int64')	UMI-collapsed inclusion junction A counts
inclB	Value('int64')	UMI-collapsed inclusion junction B counts
I	Value('int64')	max(inclA, inclB)
PSI	Value('float64')	I/(I+E)
E_ref	Value('int64')	JAseC reference E for this sample
I_ref	Value('int64')	JAseC reference I for this sample
match	Value('large_string')	OK = exact replication, MISMATCH otherwise
E_fwd	Value('int64')	sense-strand UMI count for E
E_rev	Value('int64')	antisense-strand UMI count for E
I_fwd	Value('int64')	sense-strand UMI count for I
I_rev	Value('int64')	antisense-strand UMI count for I
readsinregion	Value('int64')	reads seen in chr9:134880600-134883600
kept	Value('int64')	reads passing all JAseC filters + cell list
n_cells	Value('int64')	cells listed for this sample in cell_barcode.tsv.gz

Generation Parameters

json

{
  "script_name": "upload_valerie_artifacts.py",
  "model": "VALERIE-2.1.2 (wenweixiong/VALERIE, PlotPSI.SE.Pos)",
  "description": "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.",
  "experiment_name": "lsec-fcn2-splicing-viz",
  "cluster": "turso",
  "job_id": "turso:login-node",
  "artifact_status": "final",
  "canary": true,
  "input_datasets": [
    "depinwang/lsec-jasec-splicing-results-psi-v1"
  ],
  "hyperparameters": {}
}

Usage

python

from datasets import load_dataset

dataset = load_dataset("depinwang/lsec-fcn2-splicing-viz-pseudobulk-psi-v1", split="train")
print(f"Loaded {len(dataset)} rows")

Uploaded via [RACA](https://github.com/Zayne-sprague/Dr-Claude-Code) hf_utility.