### Create TxDb Package from TxDb Object

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Generates a complete R annotation package from an existing TxDb object. This allows for distribution and installation of custom annotation data.

```r
library(txdbmaker)

# First create a TxDb object
txdb <- makeTxDbFromUCSC(genome="sacCer3", tablename="ensGene")

# Generate default package name
pkg_name <- makePackageName(txdb)
pkg_name
# "TxDb.Scerevisiae.UCSC.sacCer3.ensGene"

# Create annotation package
makeTxDbPackage(txdb,
                version="0.99.0",
                maintainer="Your Name <your.email@example.org>",
                author="Your Name",
                destDir=".",
                license="Artistic-2.0")
```

```r
# Create package with custom name
makeTxDbPackage(txdb,
                version="1.0.0",
                maintainer="Your Name <your.email@example.org>",
                author="Your Name",
                pkgname="MyCustomTxDb",
                provider="Custom",
                providerVersion="v1")
```

--------------------------------

### Create TxDb from Ensembl for C. elegans

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object for C. elegans using data from the main Ensembl database. This is a straightforward way to get transcript annotations for a specific organism.

```R
txdb_worm <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
txdb_worm
```

--------------------------------

### Get Chromosome Information from Ensembl

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Retrieves chromosome information (chromosome name, length) for a specified dataset from Ensembl without creating a full TxDb object. Useful for quick checks of genome assembly details.

```R
chrominfo <- getChromInfoFromBiomart(dataset="celegans_gene_ensembl")
head(chrominfo)
```

--------------------------------

### Save and Load TxDb Objects

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Demonstrates how to save a TxDb object to a SQLite file and load it back. This is crucial for reproducibility and sharing annotation data.

```r
library(txdbmaker)
library(AnnotationDbi)

# Create a TxDb object
txdb <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene")

# Save TxDb to SQLite file
saveDb(txdb, file="mm9_knownGene_txdb.sqlite")

# Load TxDb from SQLite file
txdb_loaded <- loadDb("mm9_knownGene_txdb.sqlite")
txdb_loaded

# Verify the loaded object
identical(as.list(txdb), as.list(txdb_loaded))
```

```r
# Save with timestamp for reproducibility
timestamp <- format(Sys.Date(), "%Y%m%d")
saveDb(txdb, file=paste0("mm9_knownGene_", timestamp, ".sqlite"))
```

--------------------------------

### Create TxDb from Ensembl MySQL

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Constructs TxDb objects by connecting to Ensembl databases, supporting specific releases, mirrors, and filtering attributes.

```r
library(txdbmaker)

# Create TxDb from Ensembl for Yeast (current release)
txdb_yeast <- makeTxDbFromEnsembl(organism="Saccharomyces cerevisiae")
txdb_yeast

# Create TxDb for Human with specific Ensembl release
txdb_human <- makeTxDbFromEnsembl(organism="Homo sapiens",
                                   release=110)

# Use specific Ensembl server (US East mirror for faster access in Americas)
txdb_mouse <- makeTxDbFromEnsembl(organism="Mus musculus",
                                   server="useastdb.ensembl.org")

# Filter to only GENCODE basic transcripts
txdb_human_basic <- makeTxDbFromEnsembl(organism="Homo sapiens",
                                         tx_attrib="gencode_basic")

# Handle potential server synchronization issues after new release
txdb <- try(makeTxDbFromEnsembl("Saccharomyces cerevisiae",
                                 server="useastdb.ensembl.org"))
if (inherits(txdb, "try-error")) {
    txdb <- makeTxDbFromEnsembl("Saccharomyces cerevisiae",
                                 server="ensembldb.ensembl.org")
}

# Specify custom taxonomy ID
txdb_zebrafish <- makeTxDbFromEnsembl(organism="Danio rerio",
                                       taxonomyId=7955)
```

--------------------------------

### Create TxDb from GFF3 File

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from a local GFF3 file. Requires specifying the file path, data source name, and organism. The function automatically detects the GFF3 format.

```R
gff_file <- system.file("extdata", "GFF3_files", "a.gff3",
                         package="txdbmaker")
txdb_gff <- makeTxDbFromGFF(gff_file,
                             dataSource="partial gff file for testing",
                             organism="Solanum lycopersicum")
txdb_gff
```

--------------------------------

### makeTxDbFromEnsembl

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object by importing transcript annotations directly from an Ensembl MySQL database. This is the recommended method for Ensembl data as it tends to be faster and more reliable than makeTxDbFromBiomart. Requires the RMariaDB package.

```APIDOC
## makeTxDbFromEnsembl

### Description
Creates a TxDb object by importing transcript annotations directly from an Ensembl MySQL database.

### Method
Not specified (R function)

### Endpoint
Not applicable (R function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```r
library(txdbmaker)

# Create TxDb from Ensembl for Yeast (current release)
txdb_yeast <- makeTxDbFromEnsembl(organism="Saccharomyces cerevisiae")
txdb_yeast

# Create TxDb for Human with specific Ensembl release
txdb_human <- makeTxDbFromEnsembl(organism="Homo sapiens",
                                   release=110)

# Use specific Ensembl server (US East mirror for faster access in Americas)
txdb_mouse <- makeTxDbFromEnsembl(organism="Mus musculus",
                                   server="useastdb.ensembl.org")

# Filter to only GENCODE basic transcripts
txdb_human_basic <- makeTxDbFromEnsembl(organism="Homo sapiens",
                                         tx_attrib="gencode_basic")

# Handle potential server synchronization issues after new release
txdb <- try(makeTxDbFromEnsembl("Saccharomyces cerevisiae",
                                 server="useastdb.ensembl.org"))
if (inherits(txdb, "try-error")) {
    txdb <- makeTxDbFromEnsembl("Saccharomyces cerevisiae",
                                 server="ensembldb.ensembl.org")
}

# Specify custom taxonomy ID
txdb_zebrafish <- makeTxDbFromEnsembl(organism="Danio rerio",
                                       taxonomyId=7955)
```

### Response
#### Success Response (200)
Returns a TxDb object.

#### Response Example
Not specified in the provided text.
```

--------------------------------

### Create TxDb from Ensembl Protists

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object for Toxoplasma gondii using the Ensembl Protists database. Requires specifying the 'protists_mart' biomart.

```R
tgondii_txdb <- makeTxDbFromBiomart(biomart="protists_mart",
                                     dataset="tgondii_eg_gene",
                                     host="https://protists.ensembl.org")
```

--------------------------------

### Create TxDb from Remote GFF3 URL

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object directly from a GFF3 file hosted at a remote URL. This simplifies the process when annotations are available online.

```R
txdb_remote <- makeTxDbFromGFF(
    "https://example.com/annotations/species.gff3",
    dataSource="Remote annotation server",
    organism="Species name"
)
```

--------------------------------

### Create TxDb from GFF with Explicit Format Specification

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from a GFF file, explicitly specifying the format as 'gff3'. This is useful when the function's auto-detection might fail or for clarity.

```R
gff_file <- system.file("extdata", "GFF3_files", "a.gff3",
                         package="txdbmaker")
txdb_explicit <- makeTxDbFromGFF(gff_file,
                                  format="gff3",
                                  dataSource="Manual format specification",
                                  organism="Test organism")
```

--------------------------------

### List Datasets from Ensembl

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Lists available datasets in Ensembl and filters for specific organisms like C. elegans. Requires the 'ensembldb' package.

```R
mart <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL",
                   host="https://www.ensembl.org")
datasets <- listDatasets(mart)
head(datasets)
subset(datasets, grepl("elegans", dataset, ignore.case=TRUE))
```

--------------------------------

### Create TxDb from Ensembl Fungi for Yeast

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object for yeast (Saccharomyces cerevisiae) using the Ensembl Fungi database. Requires specifying the 'fungi_mart' biomart.

```R
yeast_txdb <- makeTxDbFromBiomart(biomart="fungi_mart",
                                   dataset="scerevisiae_eg_gene",
                                   host="https://fungi.ensembl.org")
```

--------------------------------

### Create TxDb from BioMart

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Retrieves annotations from BioMart databases; note that this method is being phased out in favor of Ensembl-specific functions.

```r
library(txdbmaker)
library(biomaRt)

# List available BioMart databases
listMarts(host="https://www.ensembl.org")
```

--------------------------------

### Load and Query TxDb Objects

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Load a pre-existing SQLite database and extract genomic feature ranges using standard accessor functions.

```r
txdb <- loadDb("mm9_knownGene_txdb.sqlite")
transcripts(txdb)  # Extract transcript ranges
exons(txdb)        # Extract exon ranges
cds(txdb)          # Extract CDS ranges
genes(txdb)        # Extract gene ranges
```

--------------------------------

### Create TxDb from GTF File with Custom Metadata and Chrominfo

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from a GTF file, allowing for custom metadata and chromosome information to be provided. This is useful for annotations with specific requirements or from custom sources.

```R
gtf_file <- system.file("extdata", "GTF_files",
                         "GCA_002204515.1_AaegL5.0_genomic.gtf.gz",
                         package="txdbmaker")

resource_url <- paste0("ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/204/515/",
                        "GCA_002204515.1_AaegL5.0/")
metadata <- data.frame(name="Resource URL", value=resource_url)

chrominfo <- data.frame(chrom="MF194022.1",
                        length=16790,
                        is_circular=TRUE,
                        genome="AaegL5.0")

txdb_gtf <- makeTxDbFromGFF(gtf_file,
                             dataSource="NCBI",
                             organism="Aedes aegypti",
                             chrominfo=chrominfo,
                             metadata=metadata)
```

--------------------------------

### Import GFF3 into GRanges and Convert to TxDb

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Imports a GFF3 file into a GRanges object and then converts it into a TxDb object. This approach is useful when annotation data is already in memory as a GRanges object.

```R
library(txdbmaker)
library(BiocIO)

GFF3_files <- system.file("extdata", "GFF3_files", package="txdbmaker")
path <- file.path(GFF3_files, "a.gff3")
gr <- import(path)
txdb <- makeTxDbFromGRanges(gr)
txdb
```

--------------------------------

### Generate and save a TxDb object from UCSC

Source: https://github.com/bioconductor/txdbmaker/blob/devel/inst/extdata/README.txt

Creates a TxDb object from the sacCer2 genome and sgdGene table, then saves it to a local SQLite file.

```R
txdb <- makeTxDbFromUCSC(genome="sacCer2", tablename="sgdGene")
saveDb(txdb, "sacCer2_sgdGene_txdb.sqlite")
```

--------------------------------

### Create TxDb from Data Frames

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Constructs a TxDb object directly from user-supplied data frames for transcripts and splicing information. This is a low-level constructor useful for custom annotation data.

```r
library(txdbmaker)

# Define transcripts data frame (required)
transcripts <- data.frame(
    tx_id = 1:3,
    tx_chrom = "chr1",
    tx_strand = c("-", "+", "+"),
    tx_start = c(1, 2001, 2001),
    tx_end = c(999, 2199, 2199),
    tx_name = c("tx1", "tx2", "tx3"),
    tx_type = c("mRNA", "mRNA", "ncRNA"),
    gene_id = c("gene1", "gene2", "gene2")
)

# Define splicings data frame (required) - exons and CDS
splicings <- data.frame(
    tx_id = c(1L, 2L, 2L, 2L, 3L, 3L),
    exon_rank = c(1, 1, 2, 3, 1, 2),
    exon_start = c(1, 2001, 2101, 2131, 2001, 2131),
    exon_end = c(999, 2085, 2144, 2199, 2085, 2199),
    cds_start = c(1, 2022, 2101, 2131, NA, NA),
    cds_end = c(999, 2085, 2144, 2193, NA, NA),
    cds_phase = c(0, 0, 2, 0, NA, NA)
)

# Create basic TxDb
txdb <- makeTxDb(transcripts, splicings)
txdb
```

```r
# Create TxDb with chromosome information
chrominfo <- data.frame(
    chrom = "chr1",
    length = 10000,
    is_circular = FALSE
)

txdb_with_chrominfo <- makeTxDb(transcripts, splicings,
                                 chrominfo=chrominfo)
```

```r
# Create TxDb with metadata
metadata <- data.frame(
    name = c("Organism", "Genome", "Data source"),
    value = c("Synthetic organism", "custom_v1", "User generated")
)

txdb_with_meta <- makeTxDb(transcripts, splicings,
                            chrominfo=chrominfo,
                            metadata=metadata)
```

```r
# Create TxDb with separate genes data frame
genes <- data.frame(
    tx_id = c(1L, 2L, 3L),
    gene_id = c("gene1", "gene2", "gene2")
)
# Note: Remove gene_id from transcripts when using genes data frame
transcripts_no_gene <- transcripts[, !names(transcripts) %in% "gene_id"]
txdb_with_genes <- makeTxDb(transcripts_no_gene, splicings, genes=genes)
```

```r
# Reassign internal IDs for consistent ordering
txdb_reassigned <- makeTxDb(transcripts, splicings, reassign.ids=TRUE)
```

--------------------------------

### Create TxDb from Ensembl for a Subset of Human Transcripts

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object for a specific subset of human transcripts by providing a list of transcript IDs. This is useful for focusing on a small set of genes.

```R
transcript_ids <- c(
    "ENST00000013894",
    "ENST00000268655",
    "ENST00000313243",
    "ENST00000435657"
)
txdb_human_subset <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
                                          transcript_ids=transcript_ids)
```

--------------------------------

### Import GTF into GRanges and Convert to TxDb

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Imports a GTF file into a GRanges object and subsequently converts it into a TxDb object. This method is efficient if the GTF data has already been parsed into a GRanges structure.

```R
library(txdbmaker)
library(BiocIO)

GTF_files <- system.file("extdata", "GTF_files", package="txdbmaker")
path <- file.path(GTF_files, "test1.gtf")
gr_gtf <- import(path)
txdb_gtf <- makeTxDbFromGRanges(gr_gtf)
```

--------------------------------

### makeTxDbFromBiomart

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from transcript annotations available on a BioMart database. Supports multiple BioMart databases including Ensembl, Ensembl Fungi, Ensembl Metazoa, Ensembl Plants, Ensembl Protists, and Gramene. Note: This function is being phased out in favor of makeTxDbFromEnsembl for Ensembl data.

```APIDOC
## makeTxDbFromBiomart

### Description
Creates a TxDb object from transcript annotations available on a BioMart database.

### Method
Not specified (R function)

### Endpoint
Not applicable (R function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```r
library(txdbmaker)
library(biomaRt)

# List available BioMart databases
listMarts(host="https://www.ensembl.org")
```

### Response
#### Success Response (200)
Returns a TxDb object.

#### Response Example
Not specified in the provided text.
```

--------------------------------

### Create TxDb from UCSC Genome Browser

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Functions for querying UCSC genome metadata and constructing TxDb objects from specific tables or transcript subsets.

```r
library(txdbmaker)
library(UCSC.utils)

# List available UCSC genomes
list_UCSC_genomes()[ , "genome"]

# Search for human genomes
list_UCSC_genomes("human")

# Display supported tables for a genome
supportedUCSCtables("hg38")
#   tablename                track                    subtrack
# 1 knownGene           GENCODE V46           Comprehensive...
# 2 ncbiRefSeq        NCBI RefSeq                     <NA>
# 3 ncbiRefSeqCurated NCBI RefSeq            NCBI RefSeq Curated
# ...

# Open UCSC track page in browser for reference
browseUCSCtrack("hg38", tablename="knownGene")

# Create TxDb from UCSC for Yeast
txdb_yeast <- makeTxDbFromUCSC(genome="sacCer3", tablename="ensGene")
txdb_yeast
# TxDb object:
# # Db type: TxDb
# # Supporting package: GenomicFeatures
# # Genome: sacCer3
# # transcript_nrow: 7126
# # exon_nrow: 7459
# # cds_nrow: 7012
# # UCSC Table: ensGene

# Create TxDb with specific transcript IDs (partial dataset)
transcript_ids <- c(
    "uc009uzf.1",
    "uc009uzg.1",
    "uc009uzh.1",
    "uc009uzi.1",
    "uc009uzj.1"
)
txdb_mouse_partial <- makeTxDbFromUCSC(genome="mm10",
                                        tablename="knownGene",
                                        transcript_ids=transcript_ids)

# Create TxDb for human hg19 with custom circular sequences
txdb_human <- makeTxDbFromUCSC(genome="hg19",
                                tablename="knownGene",
                                circ_seqs="chrM",
                                taxonomyId=9606)
```

--------------------------------

### Create TxDb Package Directly from UCSC

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Convenience function to create an R annotation package directly from UCSC genome data. Simplifies the process of generating shareable annotation packages.

```r
makeTxDbPackageFromUCSC(version="0.01",
                         maintainer="Some One <so@someplace.org>",
                         author="Some One",
                         genome="sacCer2",
                         tablename="ensGene")
```

--------------------------------

### Round-trip: Convert TxDb back to GRanges

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Demonstrates converting a TxDb object back into a GRanges object using the asGFF function. This is useful for exporting or further manipulating the annotation data in a GRanges format.

```R
library(txdbmaker)
library(BiocIO)

GFF3_files <- system.file("extdata", "GFF3_files", package="txdbmaker")
path <- file.path(GFF3_files, "a.gff3")
gr <- import(path)
txdb <- makeTxDbFromGRanges(gr)

gr_exported <- asGFF(txdb)
```

--------------------------------

### Create TxDb from GRanges with Custom Metadata

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from a GRanges object, incorporating custom metadata. This allows for richer annotation information to be associated with the transcript database.

```R
library(txdbmaker)
library(BiocIO)

GFF3_files <- system.file("extdata", "GFF3_files", package="txdbmaker")
path <- file.path(GFF3_files, "a.gff3")
gr <- import(path)

custom_metadata <- data.frame(
    name = c("Data source", "Creation date"),
    value = c("Custom annotation", as.character(Sys.Date()))
)
txdb_with_meta <- makeTxDbFromGRanges(gr, metadata=custom_metadata)
```

--------------------------------

### makeTxDbFromUCSC

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from transcript annotations available at the UCSC Genome Browser. This function downloads annotation tables for a specified genome assembly and converts them into a queryable TxDb object. Requires the RMariaDB package for database connectivity.

```APIDOC
## makeTxDbFromUCSC

### Description
Creates a TxDb object from transcript annotations available at the UCSC Genome Browser.

### Method
Not specified (R function)

### Endpoint
Not applicable (R function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```r
library(txdbmaker)
library(UCSC.utils)

# List available UCSC genomes
list_UCSC_genomes()[ , "genome"]

# Search for human genomes
list_UCSC_genomes("human")

# Display supported tables for a genome
supportedUCSCtables("hg38")

# Browse UCSC track page in browser for reference
browseUCSCtrack("hg38", tablename="knownGene")

# Create TxDb from UCSC for Yeast
txdb_yeast <- makeTxDbFromUCSC(genome="sacCer3", tablename="ensGene")
txdb_yeast

# Create TxDb with specific transcript IDs (partial dataset)
transcript_ids <- c(
    "uc009uzf.1",
    "uc009uzg.1",
    "uc009uzh.1",
    "uc009uzi.1",
    "uc009uzj.1"
)
txdb_mouse_partial <- makeTxDbFromUCSC(genome="mm10",
                                        tablename="knownGene",
                                        transcript_ids=transcript_ids)

# Create TxDb for human hg19 with custom circular sequences
txdb_human <- makeTxDbFromUCSC(genome="hg19",
                                tablename="knownGene",
                                circ_seqs="chrM",
                                taxonomyId=9606)
```

### Response
#### Success Response (200)
Returns a TxDb object.

#### Response Example
```
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Genome: sacCer3
# transcript_nrow: 7126
# exon_nrow: 7459
# cds_nrow: 7012
# UCSC Table: ensGene
```
```

--------------------------------

### Create TxDb Package from BioMart

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Generates an R annotation package from BioMart data, allowing for subsetting transcripts by ID. Useful for creating focused annotation packages.

```r
transcript_ids <- c(
    "ENST00000400839",
    "ENST00000400840",
    "ENST00000478783"
)
makeTxDbPackageFromBiomart(version="0.01",
                            maintainer="Some One <so@someplace.org>",
                            author="Some One",
                            transcript_ids=transcript_ids)
```

--------------------------------

### Recreate TxDb from GRanges

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Recreates a TxDb object from an existing GRanges object. Useful for filtering or modifying annotation data.

```r
txdb_recreated <- makeTxDbFromGRanges(gr_exported)
```

--------------------------------

### Create TxDb from GFF using DbxrefTag for Gene IDs

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from a GFF file, using the 'dbxrefTag' argument to specify which attribute in the Dbxref field should be used for gene IDs. This is common for NCBI annotations.

```R
txdb_ncbi <- makeTxDbFromGFF("path/to/ncbi_annotation.gff",
                              dbxrefTag="GeneID",
                              organism="Organism name")
```

--------------------------------

### Create FeatureDb Package from UCSC Track

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a FeatureDb annotation package from a specific UCSC track. This is useful for creating packages for non-gene features like tRNAs.

```r
makeFDbPackageFromUCSC(version="0.01",
                        maintainer="Some One <so@someplace.org>",
                        author="Some One",
                        genome="hg19",
                        track="tRNAs",
                        tablename="tRNAs")
```

--------------------------------

### Create FeatureDb from UCSC Tracks

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Construct a FeatureDb object by querying UCSC genome tracks. Note that this functionality is currently deprecated.

```r
library(txdbmaker)
library(UCSC.utils)

# Display available genomes
list_UCSC_genomes()[ , "genome"]

# Display available tracks for a genome
list_UCSC_tracks("mm10")

# Find the primary table for a specific track
subset(list_UCSC_tracks("mm10"), track == "qPCR Primers")

# Display table schema to see available columns
UCSCFeatureDbTableSchema(genome="mm10", tablename="qPcrPrimers")
# Returns named character vector of column types

# Create FeatureDb from UCSC track
fdb <- makeFeatureDbFromUCSC(genome="mm10",
                              tablename="qPcrPrimers")
fdb

# Create FeatureDb with custom column specification
columns <- UCSCFeatureDbTableSchema(genome="hg19", tablename="tRNAs")
fdb_trna <- makeFeatureDbFromUCSC(genome="hg19",
                                   tablename="tRNAs",
                                   columns=columns)

# Specify custom chromosome column names (for non-standard tables)
fdb_custom <- makeFeatureDbFromUCSC(genome="hg19",
                                     tablename="knownGene",
                                     chromCol="chrom",
                                     chromStartCol="txStart",
                                     chromEndCol="txEnd")
```

--------------------------------

### Create TxDb from GRanges with Taxonomy ID

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from a GRanges object, specifying a taxonomy ID for accurate organism annotation. This ensures correct biological context for the transcript data.

```R
library(txdbmaker)
library(BiocIO)

GFF3_files <- system.file("extdata", "GFF3_files", package="txdbmaker")
path <- file.path(GFF3_files, "a.gff3")
gr <- import(path)
txdb_with_taxid <- makeTxDbFromGRanges(gr, taxonomyId=4081)
```

--------------------------------

### Create TxDb from GRanges, Dropping Stop Codons

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object from a GRanges object derived from GTF data, with an option to drop stop codons from CDS features. This is a GTF-specific option for refining coding sequence annotations.

```R
library(txdbmaker)
library(BiocIO)

GTF_files <- system.file("extdata", "GTF_files", package="txdbmaker")
path <- file.path(GTF_files, "test1.gtf")
gr_gtf <- import(path)
txdb_no_stop <- makeTxDbFromGRanges(gr_gtf, drop.stop.codons=TRUE)
```

--------------------------------

### Create TxDb from Ensembl with Gene ID Filter

Source: https://context7.com/bioconductor/txdbmaker/llms.txt

Creates a TxDb object for human genes, filtering to include only a specific gene based on its Ensembl gene ID. This allows for targeted annotation retrieval.

```R
my_filter <- list(ensembl_gene_id="ENSG00000011198")
txdb_filtered <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
                                      filter=my_filter)
```

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