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huangkuanlin 7f94783fab Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation

- Introduced a comprehensive RNA velocity analysis pipeline using scVelo, including data loading, preprocessing, velocity estimation, and visualization.
- Added a script for running RNA velocity analysis with customizable parameters and output options.
- Created detailed documentation for IQ-TREE 2 phylogenetic inference, covering command syntax, model selection, bootstrapping methods, and output interpretation.
- Included references for velocity models and their mathematical framework, along with a comparison of different models.
- Enhanced the scVelo skill documentation with installation instructions, use cases, and best practices for RNA velocity analysis.

2026-03-03 07:15:36 -05:00

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cBioPortal Study Exploration Reference

Major Study Collections

TCGA (The Cancer Genome Atlas)

Study ID	Cancer Type	Samples
`brca_tcga`	Breast Cancer	~1,000
`luad_tcga`	Lung Adenocarcinoma	~500
`lusc_tcga`	Lung Squamous Cell Carcinoma	~500
`coadread_tcga`	Colorectal Cancer	~600
`gbm_tcga`	Glioblastoma	~600
`prad_tcga`	Prostate Cancer	~500
`skcm_tcga`	Skin Cutaneous Melanoma	~450
`blca_tcga`	Bladder Urothelial Carcinoma	~400
`hnsc_tcga`	Head and Neck Squamous	~500
`lihc_tcga`	Liver Hepatocellular Carcinoma	~370
`stad_tcga`	Stomach Adenocarcinoma	~440
`ucec_tcga`	Uterine Endometrial Carcinoma	~550
`ov_tcga`	Ovarian Serous Carcinoma	~580
`kirc_tcga`	Kidney Renal Clear Cell Carcinoma	~530
`thca_tcga`	Thyroid Cancer	~500
`paad_tcga`	Pancreatic Adenocarcinoma	~180
`laml_tcga`	Acute Myeloid Leukemia	~200
`acc_tcga`	Adrenocortical Carcinoma	~90

TCGA Pan-Cancer

Study ID	Description
`tcga_pan_can_atlas_2018`	TCGA Pan-Cancer Atlas (32 cancer types, ~10K samples)

MSK-IMPACT (Memorial Sloan Kettering)

Study ID	Description
`msk_impact_2017`	MSK-IMPACT clinical sequencing
`mskcc_pd`	MSK pediatric solid tumors

AACR Project GENIE

Study ID	Description
`genie_14_1_public`	GENIE v14.1 (multi-center clinical sequencing)

Molecular Profile ID Naming Conventions

Molecular profile IDs are structured as {studyId}_{type}:

Type Suffix	Alteration Type
`_mutations`	Somatic mutations (MAF)
`_gistic`	Copy number (GISTIC discrete: -2, -1, 0, 1, 2)
`_cna`	Copy number (continuous log2 ratio)
`_mrna`	mRNA expression (z-scores or log2)
`_rna_seq_v2_mrna`	RNA-seq (RSEM)
`_rna_seq_v2_mrna_median_Zscores`	RNA-seq z-scores relative to normals
`_rppa`	RPPA protein expression
`_rppa_Zscores`	RPPA z-scores
`_sv`	Structural variants/fusions
`_methylation_hm450`	DNA methylation (450K array)

Example: For brca_tcga:

brca_tcga_mutations — mutation data
brca_tcga_gistic — CNA data
brca_tcga_rna_seq_v2_mrna — RNA-seq expression

Each study has sample lists of different subsets:

Category	sampleListId Pattern	Contents
`all_cases_in_study`	`{studyId}_all`	All samples
`all_cases_with_mutation_data`	`{studyId}_sequenced`	Sequenced samples only
`all_cases_with_cna_data`	`{studyId}_cna`	Samples with CNA data
`all_cases_with_mrna_data`	`{studyId}_mrna`	Samples with expression
`all_cases_with_rppa_data`	`{studyId}_rppa`	Samples with RPPA
`all_complete_cases`	`{studyId}_complete`	Complete multiplatform data

Common Gene Entrez IDs

Gene	Entrez ID	Role
TP53	7157	Tumor suppressor
PIK3CA	5290	Oncogene
KRAS	3845	Oncogene
BRCA1	672	Tumor suppressor
BRCA2	675	Tumor suppressor
PTEN	5728	Tumor suppressor
EGFR	1956	Oncogene
MYC	4609	Oncogene
RB1	5925	Tumor suppressor
APC	324	Tumor suppressor
CDKN2A	1029	Tumor suppressor
IDH1	3417	Oncogene (mutant)
BRAF	673	Oncogene
CDH1	999	Tumor suppressor
VHL	7428	Tumor suppressor

Mutation Type Classifications

mutationType	Description
`Missense_Mutation`	Amino acid change
`Nonsense_Mutation`	Premature stop codon
`Frame_Shift_Del`	Frameshift deletion
`Frame_Shift_Ins`	Frameshift insertion
`Splice_Site`	Splice site mutation
`In_Frame_Del`	In-frame deletion
`In_Frame_Ins`	In-frame insertion
`Translation_Start_Site`	Start codon mutation
`Nonstop_Mutation`	Stop codon mutation
`Silent`	Synonymous
`5'Flank`	5' flanking
`3'UTR`	3' UTR

OncoPrint Color Legend

cBioPortal uses consistent colors in OncoPrint:

Red: Amplification
Blue (dark): Deep deletion
Green: Missense mutation
Black: Truncating mutation
Purple: Fusion
Orange: mRNA upregulation
Teal: mRNA downregulation

4.3 KiB Raw Blame History