菜单
Gene annotations and TSS analysis using gcell. Use this skill when users ask about: - GENCODE gene annotations - Transcription start sites (TSS) - Gene coordinates and metadata - Transcript information - Querying genes by genomic region Triggers: gene annotation, GENCODE, TSS, transcription start site, gene coordinates, transcript, GTF
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基于 SOC 职业分类
| name | gcell-gene |
| description | Gene annotations and TSS analysis using gcell. Use this skill when users ask about: - GENCODE gene annotations - Transcription start sites (TSS) - Gene coordinates and metadata - Transcript information - Querying genes by genomic region Triggers: gene annotation, GENCODE, TSS, transcription start site, gene coordinates, transcript, GTF |
| refs | ["_refs/gencode-gene-api.md"] |
from gcell.rna.gencode import Gencode
# Load annotations for specific genome
gencode = Gencode(assembly="hg38") # Human GRCh38
gencode = Gencode(assembly="hg19") # Human GRCh37
gencode = Gencode(assembly="mm10") # Mouse mm10
# Get gene by symbol
gene = gencode.get_gene("TP53")
gene = gencode.get_gene("BRCA1")
gene = gencode.get_gene("MYC")
# Gene attributes
print(gene.id) # Ensembl ID: "ENSG00000141510"
print(gene.name) # Symbol: "TP53"
print(gene.chrom) # Chromosome: "chr17"
print(gene.strand) # Strand: "-"
# Gene coordinates
print(gene.tss_coordinate) # Primary TSS coordinate
print(gene.tes) # Primary TES coordinate
# Full gene body
chrom, start, end, strand = gene.genomic_range
# Get list of TSS objects (one per transcript)
for tss in gene.tss:
print(tss.chrom, tss.start, tss.strand)
# Get primary TSS coordinate
tss_coord = gene.tss_coordinate
# Access TSS DataFrame for detailed info
print(gene.tss_list) # DataFrame with Chromosome, Start, End, Strand, gene_name, gene_id
# Find genes in a genomic region
result = gencode.query_region("chr17", 41196312, 41277500)
# Returns DataFrame with matching genes
print(result[['gene_name', 'Chromosome', 'Start', 'End', 'Strand']])
# Quick lookups without creating Gene objects
strand = gencode.gene_to_strand["TP53"] # "-"
chrom = gencode.gene_to_chrom["TP53"] # "chr17"
tss = gencode.gene_to_tss["TP53"] # 7687538
tes = gencode.gene_to_tes["TP53"] # 7668421
gene_type = gencode.gene_to_type["TP53"] # "protein_coding"
gene_id = gencode.gene_to_id["TP53"] # "ENSG00000141510"
| Class | Purpose |
|---|---|
Gencode | GENCODE annotation database |
Gene | Gene with coordinates and TSS/TES |
TSS | Transcription start site object |
GeneSets | Collection of Gene objects |
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