msigdbr

https://igordot.github.io/msigdbr/
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msigdbr is an R package that provides Molecular Signatures Database (MSigDB) gene sets in a tidy...
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### Install msigdbr Package

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

Install the msigdbr package from CRAN. This is the first step before using the package.

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

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

### Retrieve Hallmark Gene Sets for Mouse

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

Filter gene sets by specifying the 'collection' parameter. This example retrieves the Hallmark gene sets for mouse.

```R
h_gene_sets <- msigdbr(species = "mouse", collection = "H")
```

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

### Get CGP Gene Sets for Rattus norvegicus

Source: https://igordot.github.io/msigdbr/reference/msigdbr.html

Use this function to retrieve CGP gene sets. Ensure the `msigdbr` package is installed. The output includes gene symbols mapped to rat orthologs.

```r
gs <- msigdbr(species = "Rattus norvegicus", collection = "C2", subcollection = "CGP")
head(gs)
```

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

### Retrieve C2 CGP Gene Sets for Mouse

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

Filter gene sets by specifying both 'collection' and 'subcollection' parameters. This example retrieves the C2 (curated) CGP (chemical and genetic perturbations) gene sets for mouse.

```R
cgp_gene_sets <- msigdbr(species = "mouse", collection = "C2", subcollection = "CGP")
```

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

### GET msigdbr_collections

Source: https://igordot.github.io/msigdbr/reference/msigdbr_collections.html

Retrieves a data frame of available gene set collections for a specified species.

```APIDOC
## GET msigdbr_collections

### Description
List the collections available in the msigdbr package for a given species.

### Method
GET

### Endpoint
msigdbr_collections(db_species)

### Parameters
#### Query Parameters
- **db_species** (string) - Optional - Species abbreviation for the human or mouse databases ("HS" or "MM"). Defaults to "HS".

### Response
#### Success Response (200)
- **db_version** (string) - Database version identifier.
- **gs_collection** (string) - Gene set collection code.
- **gs_subcollection** (string) - Gene set subcollection code.
- **gs_collection_name** (string) - Descriptive name of the collection.
- **num_genesets** (integer) - Number of gene sets in the collection.
```

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

### Load msigdbr Package

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

Load the msigdbr package into your R session. This is required before calling any of its functions.

```r
library(msigdbr)
```

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

### Prepare gene sets for GSVA (gsvaParam)

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

This prepares the gene sets as a list of gene symbols for use with the gsvaParam function in the GSVA package. Ensure msigdbr_df is loaded.

```r
msigdbr_list <- split(x = msigdbr_df$gene_symbol, f = msigdbr_df$gs_name)
gsvapar <- gsvaParam(geneSets = msigdbr_list, ...)
gsva(gsvapar)
```

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

### Prepare gene sets for fgsea

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

This prepares the gene sets as a list of gene symbols, suitable for the fgsea package. Ensure msigdbr_df is loaded.

```r
msigdbr_list <- split(x = msigdbr_df$gene_symbol, f = msigdbr_df$gs_name)
fgsea(pathways = msigdbr_list, ...)
```

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

### Prepare gene sets for clusterProfiler (Gene Symbols)

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

Use this when your gene IDs are gene symbols. Ensure msigdbr_df is loaded and contains the necessary columns.

```r
msigdbr_t2g <- dplyr::distinct(msigdbr_df, gs_name, gene_symbol)
enricher(gene = gene_symbols_vector, TERM2GENE = msigdbr_t2g, ...)
```

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

### Prepare gene sets for older GSVA versions

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

For GSVA versions prior to 1.50, the gsva() function can directly accept the list of gene sets. Ensure msigdbr_df is loaded.

```r
msigdbr_list <- split(x = msigdbr_df$gene_symbol, f = msigdbr_df$gs_name)
gsva(gset.idx.list = msigdbr_list, ...)
```

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

### List supported species

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

Retrieves a tibble of available species names and their common aliases.

```R
msigdbr_species()
```

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

### Prepare gene sets for clusterProfiler (Entrez IDs)

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

Use this when your gene IDs are NCBI/Entrez IDs. Ensure msigdbr_df is loaded and contains the necessary columns.

```r
msigdbr_t2g <- dplyr::distinct(msigdbr_df, gs_name, ncbi_gene)
enricher(gene = gene_ids_vector, TERM2GENE = msigdbr_t2g, ...)
```

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

### msigdbr_species() - List Species

Source: https://igordot.github.io/msigdbr/reference/index.html

This function lists the species supported by the msigdbr package.

```APIDOC
## msigdbr_species()

### Description
Lists the species available in the msigdbr package.

### Method
N/A (R function)

### Endpoint
N/A

### Parameters
N/A

### Request Example
```R
msigdbr_species()
```

### Response
#### Success Response (200)
- **character vector** - A vector of strings, where each string is the name of a supported species.
```

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

### Retrieve Mouse Gene Sets with msigdbr

Source: https://igordot.github.io/msigdbr/reference/msigdbr.html

Fetches all mouse gene sets from the MSigDB database, specifying the mouse database species and output species. Use `head()` to display the first few rows of the resulting tibble.

```r
gs <- msigdbr(db_species = "MM", species = "Mus musculus")
head(gs)
```

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

### List available species

Source: https://igordot.github.io/msigdbr/reference/msigdbr_species.html

Retrieves a data frame of species supported by the msigdbr package.

```R
msigdbr_species()
```

```R
msigdbr_species()
#> # A tibble: 20 × 2
#>    species_name                    species_common_name                          
#>    <chr>                           <chr>                                        
#>  1 Anolis carolinensis             Carolina anole, green anole                  
#>  2 Bos taurus                      bovine, cattle, cow, dairy cow, domestic cat…
#>  3 Caenorhabditis elegans          NA                                           
#>  4 Canis lupus familiaris          dog, dogs                                    
#>  5 Danio rerio                     leopard danio, zebra danio, zebra fish, zebr…
#>  6 Drosophila melanogaster         fruit fly                                    
#>  7 Equus caballus                  domestic horse, equine, horse                
#>  8 Felis catus                     cat, cats, domestic cat                      
#>  9 Gallus gallus                   bantam, chicken, chickens, Gallus domesticus 
#> 10 Homo sapiens                    human                                        
#> 11 Macaca mulatta                  rhesus macaque, rhesus macaques, Rhesus monk…
#> 12 Monodelphis domestica           gray short-tailed opossum                    
#> 13 Mus musculus                    house mouse, mouse                           
#> 14 Ornithorhynchus anatinus        duck-billed platypus, duckbill platypus, pla…
#> 15 Pan troglodytes                 chimpanzee                                   
#> 16 Rattus norvegicus               brown rat, Norway rat, rat, rats             
#> 17 Saccharomyces cerevisiae        baker's yeast, brewer's yeast, S. cerevisiae 
#> 18 Schizosaccharomyces pombe 972h- NA                                           
#> 19 Sus scrofa                      pig, pigs, swine, wild boar                  
#> 20 Xenopus tropicalis              tropical clawed frog, western clawed frog    
```

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

### Verify MSigDB Database Version

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

Check the version of the MSigDB database used in the gene set data frame.

```R
unique(all_gene_sets$db_version)
#> [1] "2026.1.Hs"
```

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

### Retrieve Gene Sets from Mouse Database

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

Specify the 'db_species' parameter to select the MSigDB database (e.g., 'MM' for mouse). The 'species' parameter still defines the orthologs to retrieve.

```R
all_mm_gene_sets <- msigdbr(db_species = "MM", species = "Mus musculus")
head(all_mm_gene_sets)
```

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

### msigdbr_collections() - List Collections

Source: https://igordot.github.io/msigdbr/reference/index.html

This function lists the available collections within the msigdbr package.

```APIDOC
## msigdbr_collections()

### Description
Lists the collections available in the msigdbr package.

### Method
N/A (R function)

### Endpoint
N/A

### Parameters
N/A

### Request Example
```R
msigdbr_collections()
```

### Response
#### Success Response (200)
- **character vector** - A vector of strings, where each string is the name of an available collection.
```

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

### List available collections

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

Retrieves a table of MSigDB collections, sub-collections, and the number of gene sets per category.

```R
msigdbr_collections()
```

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

### Retrieve Human Gene Sets with msigdbr

Source: https://igordot.github.io/msigdbr/reference/msigdbr.html

Fetches all human gene sets from the MSigDB database. Use `head()` to display the first few rows of the resulting tibble.

```r
gs <- msigdbr()
head(gs)
```

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

### Retrieve Gene Sets for Mus musculus

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

Use the 'species' parameter to convert human genes to orthologs in model organisms like Mus musculus. Use msigdbr_species() to check available species.

```R
all_gene_sets <- msigdbr(species = "Mus musculus")
head(all_gene_sets)
```

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

### List available collections

Source: https://igordot.github.io/msigdbr/reference/msigdbr_collections.html

Retrieves a data frame of available gene set collections. The db_species argument defaults to 'HS' for human.

```R
msigdbr_collections(db_species = "HS")
```

```R
msigdbr_collections()
```

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

### Retrieve All Gene Sets

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

Retrieve a data frame containing all genes and gene sets from the MSigDB. The output includes gene symbols, IDs, and detailed gene set information.

```r
all_gene_sets <- msigdbr()
head(all_gene_sets)
```

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

### Retrieve MSigDB gene sets

Source: https://igordot.github.io/msigdbr/index.html

Fetches the full set of MSigDB gene sets as a tidy data frame.

```R
library(msigdbr)
genesets <- msigdbr()
```

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

### List Available Species

Source: https://igordot.github.io/msigdbr/reference/msigdbr_species.html

This function lists all the species for which gene set enrichment data is available in the msigdbr package.

```APIDOC
## msigdbr_species()

### Description
List the species available in the msigdbr package.

### Method
Function Call

### Endpoint
N/A (R function)

### Parameters
None

### Request Example
```R
msigdbr_species()
```

### Response
#### Success Response (200)
A data frame containing the available species, with columns for `species_name` and `species_common_name`.

#### Response Example
```json
[
  {
    "species_name": "Anolis carolinensis",
    "species_common_name": "Carolina anole, green anole"
  },
  {
    "species_name": "Bos taurus",
    "species_common_name": "bovine, cattle, cow, dairy cow, domestic cat"
  }
]
```
```

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

### Retrieve species-specific gene sets

Source: https://igordot.github.io/msigdbr/index.html

Filters gene sets for a specific organism, such as mouse, by specifying the species argument.

```R
genesets <- msigdbr(species = "mouse")
```

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

### Retrieve specific gene set collections

Source: https://igordot.github.io/msigdbr/index.html

Filters gene sets by both species and collection, such as the Hallmark collection.

```R
genesets <- msigdbr(species = "mouse", collection = "H")
```

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

### msigdbr() - Retrieve Gene Sets

Source: https://igordot.github.io/msigdbr/reference/index.html

This function retrieves the gene sets data frame from the msigdbr package.

```APIDOC
## msigdbr()

### Description
Retrieves the gene sets data frame.

### Method
N/A (R function)

### Endpoint
N/A

### Parameters
N/A

### Request Example
```R
msigdbr()
```

### Response
#### Success Response (200)
- **data.frame** - A data frame containing gene set information.
```

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

### Retrieve Gene Sets Data Frame

Source: https://igordot.github.io/msigdbr/reference/msigdbr.html

This function retrieves a data frame of gene sets and their member genes. It supports converting human gene identifiers to counterparts in other model organisms and includes gene symbols along with NCBI and Ensembl IDs.

```APIDOC
## msigdbr()

### Description
Retrieve a data frame of gene sets and their member genes. The original human genes can be converted into their corresponding counterparts in various model organisms, including mouse, rat, pig, zebrafish, fly, and yeast. The output includes gene symbols along with NCBI and Ensembl IDs.

### Arguments 

- **db_species** (string) - Species abbreviation for the human or mouse databases (`"HS"` or `"MM"`).
- **species** (string) - Species name for output genes, such as `"Homo sapiens"` or `"Mus musculus"`. Both scientific and common names are acceptable. Use `msigdbr_species()` to see the available options.
- **collection** (string) - Collection abbreviation, such as `"H"` or `"C1"`. Use `msigdbr_collections()` to see the available options.
- **subcollection** (string) - Sub-collection abbreviation, such as `"CGP"` or `"BP"`. Use `msigdbr_collections()` for the available options.
- **category** (deprecated) - use the `collection` argument
- **subcategory** (deprecated) - use the `subcollection` argument

### Value
A tibble (a data frame with class `tibble::tbl_df`) of gene sets with one gene per row.

### Details
Historically, the MSigDB resource has been tailored to the analysis of human-specific datasets, with gene sets exclusively aligned to the human genome. Starting with release 2022.1, MSigDB incorporated a database of mouse-native gene sets and was split into human and mouse divisions ("Hs" and "Mm"). Each one is provided in the approved gene symbols of its respective species.
Mouse MSigDB includes gene sets curated from mouse-centric datasets and specified in native mouse gene identifiers, eliminating the need for ortholog mapping.

### References
https://www.gsea-msigdb.org/gsea/msigdb/index.jsp

### Examples
__```R
# Get all human gene sets
gs <- msigdbr()
head(gs)

# Get all mouse gene sets
gs <- msigdbr(db_species = "MM", species = "Mus musculus")
head(gs)
```__
```

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

### Filter Gene Sets using dplyr

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

The output of msigdbr() is a data frame that can be manipulated using standard methods like dplyr::filter for precise subsetting.

```R
dplyr::filter(all_gene_sets, gs_collection == "H")
```
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