Signature Collection Tutorial

Installation

Using devtools package


# Load devtools package
library(devtools)

# Install SigRepo
devtools::install_github(repo = 'montilab/SigRepo')

# Install OmicSignature
devtools::install_github(repo = 'montilab/OmicSignature')

Load packages

# Load tidyverse package
library(tidyverse)

# Load SigRepo package
library(SigRepo)

# Load OmicSignature package
library(OmicSignature)

Create a handler to connect to SigRepo Database

# Create a connection handler
conn_handler <- SigRepo::newConnHandler(
  dbname = "sigrepo", 
  host = "sigrepo.org", 
  port = 3306, 
  user = <your_username>, 
  password = <your_password>
)

Load signatures

Here, we provided 4 signature objects that came with the package for demonstrations:

omic_signature_1 (Myc_reduce_mice_liver_24m_v1)
omic_signature_2 (Myc_reduce_mice_liver_24m_v2)
omic_signature_3 (Myc_reduce_mice_liver_24m_v3)
omic_signature_4 (Myc_reduce_mice_liver_24m_v4)

# Read in the signature objects
data("omic_signature_1", package = "SigRepo")
data("omic_signature_2", package = "SigRepo")
data("omic_signature_3", package = "SigRepo")
data("omic_signature_4", package = "SigRepo")

Create an omic collection

Here, we will create a collection with two signatures, omic_signature_1 and omic_signature_1, provided above. See ?OmicSignatureCollection() from OmicSignature package for more details on how to create an omic collection object.

# Create a metadata object for the collection
metadata <- base::list(
  "collection_name" = "my_collection",
  "description" = "An example of signature collection"
)

# Create an omic collection using OmicSignatureCollection() from OmicSignature package
omic_collection <- OmicSignature::OmicSignatureCollection$new(
  OmicSigList = base::list(omic_signature_1, omic_signature_2),
  metadata = metadata
)
#>   [Success] OmicSignature Collection my_collection created.

Upload a collection to the database

The SigRepo::addCollection() function allows users to upload a collection to the database.

IMPORTANT NOTE:

The user MUST HAVE an editor or admin account to use this function.
A collection MUST BE an R6 object obtained from OmicSignature::OmicSignatureCollection()

SigRepo::addCollection(
  conn_handler = conn_handler,        # A handler contains user credentials to establish connection to a remote database
  omic_collection = omic_collection,  # An R6 object obtained from OmicSignature::OmicSignatureCollection()
  visibility = FALSE,                 # Whether to make the collection public or private. Default is FALSE.
  return_collection_id = FALSE,       # Whether to return the uploaded collection id. Default is FALSE.
  verbose = TRUE                      # Whether to print diagnostic messages. Default is TRUE.
)
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v2 created.
#>   [Success] OmicSignature Collection my_collection created.
#> Uploading each signature in the collection to the database...
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#> Error in value[[3L]](cond): Error in SigRepo::addSignature(omic_signature = omic_sig_list[[c]], conn_handler = conn_handler, : You already uploaded a signature with the name = 'Myc_reduce_mice_liver_24m_v1' (ID: '615') to the SigRepo Database.

Search for a collection in the database

The SigRepo::searchCollection() function allows users to retrieve all collections that are available in the database.

Example 1: Search for all collections

# Get all collections
collection_tbl_1 <- SigRepo::searchCollection(conn_handler = conn_handler)

# WARNINGS: THE COLLECTION TABLE CAN BE LARGE, SO ONLY THE FIRST SIX OBSERVATIONS ARE SHOWN.
if(base::nrow(collection_tbl_1) > 0){
  knitr::kable(
    utils::head(collection_tbl_1), 
    row.names = FALSE
  )
}

collection_id	collection_name	description	user_name	date_created	collection_hashkey	signature_id	signature_collection_hashkey	signature_name
61	Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024	agingâ€associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results	H_Nikoueian	2025-10-03 15:09:35	47b45086ae30d329d17ad93db68479de	213	4abdc3cd86a6f59eeb33ac7bf55252e2	Aging_Hs_HNSC_RNASeq_TCGA_ACC_MontiLab2025
61	Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024	agingâ€associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results	H_Nikoueian	2025-10-03 15:09:35	47b45086ae30d329d17ad93db68479de	214	8b4077aa6a4434add27043542cad2e8a	Aging_Hs_HNSC_RNASeq_TCGA_BLCA_MontiLab2025
61	Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024	agingâ€associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results	H_Nikoueian	2025-10-03 15:09:35	47b45086ae30d329d17ad93db68479de	215	43d0193b623ae62359f03ad342298498	Aging_Hs_HNSC_RNASeq_TCGA_BRCA_MontiLab2025
61	Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024	agingâ€associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results	H_Nikoueian	2025-10-03 15:09:35	47b45086ae30d329d17ad93db68479de	216	f984e7003314d15197a30d239df47b01	Aging_Hs_HNSC_RNASeq_TCGA_CESC_MontiLab2025
61	Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024	agingâ€associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results	H_Nikoueian	2025-10-03 15:09:35	47b45086ae30d329d17ad93db68479de	217	82fae89f903a358b58654d5e2f2d33c8	Aging_Hs_HNSC_RNASeq_TCGA_COAD_MontiLab2025
61	Aging_Hs_HNSC_RNASeq_TCGA_MontiLab2024	agingâ€associated transcriptomic signature from HPV-negative Head and Neck Squamous Cell Carcinoma (HNSC) using TCGA RNA-seq differential expression results	H_Nikoueian	2025-10-03 15:09:35	47b45086ae30d329d17ad93db68479de	218	6498fece50ede60a446812e25f080c7d	Aging_Hs_HNSC_RNASeq_TCGA_ESCA_MontiLab2025

Example 2: Search for a specific collection by its name, e.g., `collection_name = "my_collection"`.

collection_tbl_2 <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.

if(base::nrow(collection_tbl_2) > 0){
  knitr::kable(
    collection_tbl_2, 
    row.names = FALSE
  )
}

Retrieve a set of collections in the database

The SigRepo::getCollection() function allows users to retrieve a set of collections that are PUBLICLY available in the database.

IMPORTANT NOTE:

Users can ONLY RETRIEVE a list of collections that are publicly available in the database including their own uploaded collections.
If a collection is PRIVATE and belongs to other user in the database, users will need to be given an editor permission from its owner to access, retrieve, and edit their collections.

Example 1: Get all collections that are publicly available in the database

# WARNINGS: THE COLLECTION LIST CAN BE LARGE TO DOWNLOAD (NOT RUN)
collection_list_1 <- SigRepo::getCollection(conn_handler = conn_handler)

Example 2: Get a specific collection that is publicly available or owned by user in the database, e.g., `collection_name = "my_collection"`

collection_list_2 <- SigRepo::getCollection(
  conn_handler = conn_handler,
  collection_name = "my_collection"
)
#> Error in SigRepo::getCollection(conn_handler = conn_handler, collection_name = "my_collection"): 
#> There are no collection returned from the search parameters.

Update a collection metadata

The SigRepo::updateCollectionMetadata() function allows users to update the metadata information of a collection in the database.

IMPORTANT NOTE:

Users MUST HAVE an editor or admin account to use this function.
Furthermore, users can ONLY UPDATE their own uploaded signatures or were given an editor permission from its owner to access, retrieve, and edit their collections.

For example, if you want to change the description of "my_collection" in the database to "This is the updated description." You can use the SigRepo::updateCollectionMetadata() function as follows:

# Let's search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.

# If the collection exists, update it with the new description
if(base::nrow(collection_tbl) > 0){
  SigRepo::updateCollectionMetadata(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id,
    description =  "This is the updated description." 
  )
}

Now, let’s search for "my_collection" in the database and see if its description has been updated.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.

# If the collection exists, display the table
if(base::nrow(collection_tbl) > 0){
  knitr::kable(
    collection_tbl,
    row.names = FALSE
  )
}

Add signatures to an existing collection in the database

The SigRepo::addSignatureToCollection() function allows users to add a set of signatures to an existing collection in the database.

IMPORTANT NOTE:

Users MUST HAVEan editor or admin account to use this function.
Furthermore, users can ONLY UPDATE their own uploaded signatures or were given an editor permission from its owner to access, retrieve, and edit their collections.

For example, if you wish to create two new signatures ("omic_signature_3", "omic_signature_4") and add them to "my_collection"in the database.

# Add omic_signature_3 to the database
signature_id_3 <- SigRepo::addSignature(
  conn_handler = conn_handler, 
  omic_signature = omic_signature_3,
  return_signature_id = TRUE,
  verbose = FALSE
)
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v3 created.
#> Error in SigRepo::addSignature(conn_handler = conn_handler, omic_signature = omic_signature_3, : You already uploaded a signature with the name = 'Myc_reduce_mice_liver_24m_v3' (ID: '415') to the SigRepo Database.

# Add omic_signature_4 to the database
signature_id_4 <- SigRepo::addSignature(
  conn_handler = conn_handler, 
  omic_signature = omic_signature_4,
  return_signature_id = TRUE,
  verbose = FALSE
)
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v4 created.
#> Error in SigRepo::addSignature(conn_handler = conn_handler, omic_signature = omic_signature_4, : You already uploaded a signature with the name = 'Myc_reduce_mice_liver_24m_v4' (ID: '416') to the SigRepo Database.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection",
  verbose = FALSE
)

# If both collection and signatures exist, add its signature ids to collection.
if(base::nrow(collection_tbl) > 0 && base::length(signature_id_3) > 0 && base::length(signature_id_4) > 0){
  SigRepo::addSignatureToCollection(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id,
    signature_id =  c(signature_id_3, signature_id_4)
  )
}

Now, let’s search for "my_collection" in the database and see if the signatures are added to the collection.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.

# If collection exists, display the table
if(base::nrow(collection_tbl) > 0){
  knitr::kable(
    collection_tbl,
    row.names = FALSE
  )
}

Remove a list of signatures from a collection in the database

The SigRepo::removeSignatureFromCollection() function allows users to remove a list of signatures from a collection in the database.

IMPORTANT NOTE:

Users MUST HAVEan editor or admin access to use this function.
Furthermore, users can ONLY UPDATEtheir own uploaded signatures or were given an editor permission from its owner to access, retrieve, and edit their collections.

For example, if you wish to remove "Myc_reduce_mice_liver_24m_v1" from "my_collection"in the database

# Lets' check if signature = Myc_reduce_mice_liver_24m_v1 is in my_collection
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection",
  signature_name = "Myc_reduce_mice_liver_24m_v1"
)
#> There is no collection returned from the search parameters.

# If signature collection combo exists, remove the signature.
if(base::nrow(collection_tbl) > 0){
  SigRepo::removeSignatureFromCollection(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id,
    signature_id = collection_tbl$signature_id
  )
}

Now, let’s search for "my_collection" in the database and see if signatures have been removed from the collection.

# Search for my_collection in the database
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.

# If collection exists, display the table
if(base::nrow(collection_tbl) > 0){
  knitr::kable(
    collection_tbl,
    row.names = FALSE
  )
}

Delete the whole collection from the database

The SigRepo::deleteCollection() function allows users to delete a collection from the database.

IMPORTANT NOTE:

Users MUST HAVE an editor or admin account to use this function.
Furthermore, users can ONLY DELETE their own uploaded collections or were given an editor permission from other users in the database to access and delete their collection.
A collection can ONLY BE REMOVED OR DELETED one at a time.

# Search for my_collection in the database 
collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.

# If the collection exists, remove it from the database
if(base::nrow(collection_tbl) > 0){
  SigRepo::deleteCollection(
    conn_handler = conn_handler, 
    collection_id = collection_tbl$collection_id
  )
}

Finally, let’s search for "my_collection" in the database and see if the collection has been removed.

collection_tbl <- SigRepo::searchCollection(
  conn_handler = conn_handler, 
  collection_name = "my_collection"
)
#> There is no collection returned from the search parameters.

Installation

Load packages

Create a handler to connect to SigRepo Database

Load signatures

Create an omic collection

Upload a collection to the database

Search for a collection in the database

Example 1: Search for all collections

Example 2: Search for a specific collection by its name, e.g., collection_name = "my_collection".

Retrieve a set of collections in the database

Example 1: Get all collections that are publicly available in the database

Example 2: Get a specific collection that is publicly available or owned by user in the database, e.g., collection_name = "my_collection"

Update a collection metadata

Add signatures to an existing collection in the database

Remove a list of signatures from a collection in the database

Delete the whole collection from the database

Example 2: Search for a specific collection by its name, e.g., `collection_name = "my_collection"`.

Example 2: Get a specific collection that is publicly available or owned by user in the database, e.g., `collection_name = "my_collection"`