### R: Get Human Orthologs for a Gene

Source: https://igordot.github.io/babelgene/reference/orthologs.html

Retrieve human orthologs for a given gene symbol. This example shows how to find the human equivalent of a mouse gene.

```R
orthologs(genes = "TP53", species = "mouse", human = TRUE)
#>   human_symbol human_entrez   human_ensembl taxon_id symbol entrez
#> 1         TP53         7157 ENSG00000141510    10090  Trp53  22059
#>              ensembl
#> 1 ENSMUSG00000059552
#>                                                                                         support
#> 1 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#>   support_n
#> 1        12
```

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

### Install babelgene R Package

Source: https://igordot.github.io/babelgene/articles/babelgene-intro.html

Install the babelgene R package from CRAN. This is the first step to using the package's functionalities.

```r
install.packages("babelgene")
```

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

### Load babelgene R Package

Source: https://igordot.github.io/babelgene/articles/babelgene-intro.html

Load the babelgene package into your R session to access its functions. This should be done after installation.

```r
library(babelgene)
```

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

### R: Get Non-Human Orthologs for Human Genes

Source: https://igordot.github.io/babelgene/reference/orthologs.html

Retrieve non-human orthologs for a set of human genes. This example demonstrates finding mouse equivalents for human gene symbols, with `human = FALSE` indicating the input genes are human.

```R
orthologs(genes = c("Ptprc", "Cd34"), species = "mouse", human = FALSE)
#>   human_symbol human_entrez   human_ensembl taxon_id symbol entrez
#> 1         CD34          947 ENSG00000174059    10090   Cd34  12490
#> 2        PTPRC         5788 ENSG00000081237    10090  Ptprc  19264
#>              ensembl
#> 1 ENSMUSG00000016494
#> 2 ENSMUSG00000026395
#>                                                                                         support
#> 1 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#> 2                   EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther
#>   support_n
#> 1        12
#> 2        10
```

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

### List All Available Species

Source: https://igordot.github.io/babelgene/reference/species.html

Call the `species()` function without arguments to get a data frame of all species with available human orthologs. This includes their taxon ID, scientific name, and common name.

```r
species()
```

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

### Get Mouse Orthologs for Human Genes

Source: https://igordot.github.io/babelgene/articles/babelgene-intro.html

Use the `orthologs()` function to find mouse equivalents for a list of human genes. The function returns a data frame with gene symbols and IDs for both human and mouse.

```r
orthologs(genes = c("TP53", "EGFR", "IL6", "TGFB1", "CD4"), species = "mouse")
```

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

### Get Fruit Fly Orthologs for Non-Human Genes

Source: https://igordot.github.io/babelgene/articles/babelgene-intro.html

Use the `orthologs()` function to find fruit fly equivalents for a gene symbol that is not human. Specify `human = FALSE` if the input gene is not human.

```r
orthologs(genes = "Pu", species = "fruit fly", human = FALSE)
```

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

### Filter Species by Scientific Name

Source: https://igordot.github.io/babelgene/reference/species.html

To retrieve results for a specific species, provide its scientific name as an argument to the `species()` function. For example, `species("Mus musculus")` will return only data for the mouse.

```r
species("Mus musculus")
```

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

### Filter Species by Alternative Common Name

Source: https://igordot.github.io/babelgene/reference/species.html

You can use alternative common names to filter species. For example, `species("rat")` will return data for Rattus norvegicus, including its various common names.

```r
species("rat")
```

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

### BibTeX Citation for babelgene

Source: https://igordot.github.io/babelgene/authors.html

This is the BibTeX entry for citing the babelgene R package in academic work. It includes the title, author, year, package version, and URL.

```bibtex
@Manual{
  title = {babelgene: Gene Orthologs for Model Organisms in a Tidy Data Format},
  author = {Igor Dolgalev},
  year = {2022},
  note = {R package version 22.9},
  url = {https://igordot.github.io/babelgene/},
}
```

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

### Retrieve Available Species

Source: https://igordot.github.io/babelgene/reference/species.html

Lists all available species with human orthologs. You can optionally filter by a specific species name.

```APIDOC
## species

### Description
Lists the species with available human orthologs. Can be filtered by a specific species name.

### Method
```
species(species = NULL)
```

### Parameters
#### Arguments
- **species** (string) - Optional - Species name, such as `Mus musculus` or `mouse`. If specified, will return results for the given species only.

### Returns
A data frame of the available species.

### Examples
```R
species()

species("Mus musculus")

species("mouse")

species("rat")
```
```

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

### Find Orthologs by Gene ID

Source: https://igordot.github.io/babelgene/articles/babelgene-intro.html

Use the `orthologs()` function to find orthologs for a given gene ID (NCBI Entrez or Ensembl). The `species` parameter is required, and `human = TRUE` can be set to include human gene information.

```r
orthologs(genes = "ENSG00000111640", species = "mouse", human = TRUE)
```

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

### orthologs

Source: https://igordot.github.io/babelgene/reference/orthologs.html

Retrieves gene orthologs/homologs for a set of genes, enabling conversion between human and non-human gene analogs. It allows specifying the target species, whether the input genes are human, minimum database support, and whether to return only the top match.

```APIDOC
## orthologs

### Description
Retrieve gene orthologs/homologs for a set of genes. Converts between human and non-human analogs.

### Usage
```R
orthologs(genes, species, human = TRUE, min_support = 3, top = TRUE)
```

### Arguments

* **genes** (vector) - A vector of gene symbols or Entrez/Ensembl IDs.
* **species** (string) - Species name, such as `Mus musculus` or `mouse` (see `species()` for options).
* **human** (logical scalar) - A logical scalar indicating if the input genes are human. If `TRUE`, the input genes are human. If `FALSE`, the input genes correspond to the non-human species and the output will be the human equivalents.
* **min_support** (numeric) - Minimum number of supporting source databases. Gene pairs available in this package are supported by 2 to 12 databases (the maximum varies depending on the species).
* **top** (logical) - For each gene, output only the match with the highest support level if there are multiple hits.

### Value
A data frame of gene pairs (human and given species).

### Examples
```R
orthologs(genes = "TP53", species = "mouse", human = TRUE)
orthologs(genes = c("Ptprc", "Cd34"), species = "mouse", human = FALSE)
```
```

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

### Filter Species by Common Name

Source: https://igordot.github.io/babelgene/reference/species.html

The `species()` function also accepts common names for filtering. For instance, `species("mouse")` will yield the same results as specifying the scientific name.

```r
species("mouse")
```

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