BiocOV: an overview of Bioconductor for Genomic Data Science

Vincent J. Carey, stvjc at channing.harvard.edu

May 02, 2023

Source: vignettes/BiocOV.Rmd

Introduction

This package includes vignettes, functions and illustrative data on the following topics

  • MultiAssayExperiment representation of The Cancer Genome Atlas, with illustration of survival analysis

  • Genome representation with Biostrings, BSgenome, and TxDb packages
> TxDb.Hsapiens.UCSC.hg38.knownGene
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: hg38
# Organism: Homo sapiens
# Taxonomy ID: 9606
# UCSC Table: knownGene
# UCSC Track: GENCODE V43
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Entrez Gene ID
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 274031
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2023-03-16 20:07:54 +0000 (Thu, 16 Mar 2023)
# GenomicFeatures version at creation time: 1.51.4
# RSQLite version at creation time: 2.3.0
# DBSCHEMAVERSION: 1.2

  • Single-cell transcriptomics with scRNAseq and scater, including exploration of the Human Cell Atlas, Cell Ontology, and the OSCA book.

Other topics should be proposed and added over time.