How to use the TxDb.Hsapiens.UCSC.hg38.knownGene package in R?

To use the TxDb.Hsapiens.UCSC.hg38.knownGene package in R, you will need to follow these steps: :joy: https://www.markdownguide.org/basic-syntax/ https://www.markdownguide.org/extended-syntax/ | Syntax | Description | | ----------- | ----------- | | Header | Title | | Paragraph | Text |

• Install the TxDb.Hsapiens.UCSC.hg38.knownGene package from Bioconductor using the following code:

r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene") ```r if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene") ```

• Load the package using the library() function:

r library(TxDb.Hsapiens.UCSC.hg38.knownGene)

• Load the GenomicFeatures package, which is required by TxDb packages:

r library(GenomicFeatures)

• Use the TxDb.Hsapiens.UCSC.hg38.knownGene package to create a transcript database object using the TxDb() function:

r txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

• This will create a TxDb object that contains information about gene models and transcripts from the hg38 version of the human genome, based on the knownGene track in the UCSC Genome Browser.
• You can then use the GenomicFeatures package to retrieve information about genes and transcripts from the TxDb object. For example, you can use the exonsBy() function to retrieve exon coordinates for a given gene:

r gene <- "ENSG00000139618" exons <- exonsBy(txdb, gene)

This will retrieve the exon coordinates for the gene with the Ensembl ID "ENSG00000139618".

Note that the TxDb objects can be memory-intensive, especially for larger genomes or datasets, so you may need to be careful about the amount of data you load into memory at once. You can also use the saveDb() and loadDb() functions to save and load TxDb objects to/from disk, respectively.

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