A gene-level annotation dataset derived from the UCSC knownGene and kgXref tables
for the hg38 or mm10 genome assembly. This data aggregates transcript-level information into
gene-level summary statistics, including transcript span, CDS length, and average values
across isoforms. It is the hg38 equivalent of refGenes_hg19,
or mm10 equivalent of refGenes_mm9, updated using Ensembl-based
transcript IDs from GENCODE.
These objects are tibbles (tbl_df) and inherit from data.frame.
Format
A tibble with one row per gene and the following columns:
- name2
Gene symbol (e.g., A1CF)
- chrom
Chromosome (e.g., chr10)
- strand
Strand direction, "+" or "-"
- min_txStart
Minimum transcript start position across all isoforms
- max_txEnd
Maximum transcript end position across all isoforms
- minmax_TxLen
Gene length computed as max_txEnd - min_txStart
- average_TxLen
Average transcript length across isoforms
- name
Transcript ID (typically Ensembl ID in hg38, e.g., ENST00000...)
- min_cdsStart
Minimum CDS start position
- max_cdsEnd
Maximum CDS end position
- minmax_CdsLen
CDS length computed as max_cdsEnd - min_cdsStart
- average_CdsLen
Average CDS length across isoforms
An object of class tbl_df (inherits from tbl, data.frame) with 55316 rows and 12 columns.
Source
UCSC Genome Browser: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/
UCSC Genome Browser: https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/