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
utils::data("omic_signature_1", package = "SigRepo")
utils::data("omic_signature_2", package = "SigRepo")
utils::data("omic_signature_3", package = "SigRepo")
utils::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.
)
#> Checking Signature:  Myc_reduce_mice_liver_24m_v1
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#> Checking Signature:  Myc_reduce_mice_liver_24m_v2
#>   [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...
#> Uploading Signature:  Myc_reduce_mice_liver_24m_v1
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v2 created.
#> Uploading collection metadata to the database...
#> Adding user to collection access table in the database...
#> Adding signature to the collection access table of the database...
#> Finished uploading.
#> ID of the uploaded collection: 462

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
63	Aging_4mosc1_YAPTAZ_MontiLab2024	either siYap1 (YAP KD), siWwtr1 (TAZ KD), siYap1 + siWwtr1 (YAP/TAZ KD) or siControl (Control) in 4MOSC1 cells	H_Nikoueian	2025-10-06 00:46:12	9ccbe9e91eebb32743633d64eed5a37d	278	7edc2de170157fa2d1ea167ae15f1734	Aging_4mosc1_YAP_KD_vs_Control_MontiLab2024
63	Aging_4mosc1_YAPTAZ_MontiLab2024	either siYap1 (YAP KD), siWwtr1 (TAZ KD), siYap1 + siWwtr1 (YAP/TAZ KD) or siControl (Control) in 4MOSC1 cells	H_Nikoueian	2025-10-06 00:46:12	9ccbe9e91eebb32743633d64eed5a37d	279	c48f5a2d585c74f35c5abee9a8182559	Aging_4mosc1_TAZ_KD_vs_Control_MontiLab2024
63	Aging_4mosc1_YAPTAZ_MontiLab2024	either siYap1 (YAP KD), siWwtr1 (TAZ KD), siYap1 + siWwtr1 (YAP/TAZ KD) or siControl (Control) in 4MOSC1 cells	H_Nikoueian	2025-10-06 00:46:12	9ccbe9e91eebb32743633d64eed5a37d	280	9d5cc282ed8d39ab1f15b2338af14cb2	Aging_4mosc1_YAPTAZ_KD_vs_Control_MontiLab2024
64	Aging_4mosc1_vt104_vs_DMSO_Invivo&InVitro_MontiLab2024	VT104 treatment versus DMSO in tdTomato-4MOSC1 tumors from aged mice and in vitro 4MOSC1 cells	H_Nikoueian	2025-10-06 00:48:19	1a6f64e2bc303cf9a5d56d6e553e3332	281	9a44100c280747961774218de69d688c	Aging_4mosc1_vt104_vs_DMSO_Invivo_MontiLab2024
64	Aging_4mosc1_vt104_vs_DMSO_Invivo&InVitro_MontiLab2024	VT104 treatment versus DMSO in tdTomato-4MOSC1 tumors from aged mice and in vitro 4MOSC1 cells	H_Nikoueian	2025-10-06 00:48:19	1a6f64e2bc303cf9a5d56d6e553e3332	282	21058d1ceace59afaafa77683f7ad4c0	Aging_4mosc1_vt104_vs_DMSO_InVitro_MontiLab2024
65	Oralcancer_Hs_HSC3_YAPTAZ_DPAGT1_MontiLab2022	TAZ, YAP, T+Y and DPAGT1 KD experiments in HSC3 HNSCC cancer cells	H_Nikoueian	2025-10-06 15:15:44	52b08fcc2980cb6a8212e24a6e2e05a2	283	41e9c697b36c6b038a95c7139e59fde3	Oralcancer_Hs_HSC3_TAZ_vs_control_MontiLab2022

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"
)

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

collection_id	collection_name	description	user_name	date_created	visibility	collection_hashkey	signature_id	signature_collection_hashkey	signature_name
462	my_collection	An example of signature collection	montilab	2026-01-27 16:03:43	0	a7213731b133effec506851ef7cb443f	414	dcb983859cddb392e870425335dc5b51	Myc_reduce_mice_liver_24m_v2
462	my_collection	An example of signature collection	montilab	2026-01-27 16:03:43	0	a7213731b133effec506851ef7cb443f	615	1e2b12ca47f7ae90387a2aabf7bce2cf	Myc_reduce_mice_liver_24m_v1

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"
)
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v2 created.
#>   [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#>   [Success] OmicSignature Collection my_collection created.

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"
)

# 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." 
  )
}
#> collection_id = '462' has been updated.

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"
)

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

collection_id	collection_name	description	user_name	date_created	visibility	collection_hashkey	signature_id	signature_collection_hashkey	signature_name
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	0	a7213731b133effec506851ef7cb443f	414	dcb983859cddb392e870425335dc5b51	Myc_reduce_mice_liver_24m_v2
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	0	a7213731b133effec506851ef7cb443f	615	1e2b12ca47f7ae90387a2aabf7bce2cf	Myc_reduce_mice_liver_24m_v1

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.

# 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.

# 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"
)

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

collection_id	collection_name	description	user_name	date_created	collection_hashkey	signature_id	signature_collection_hashkey	signature_name
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	a7213731b133effec506851ef7cb443f	414	dcb983859cddb392e870425335dc5b51	Myc_reduce_mice_liver_24m_v2
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	a7213731b133effec506851ef7cb443f	415	84b1e6d75210adac4c113f5fd0f66324	Myc_reduce_mice_liver_24m_v3
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	a7213731b133effec506851ef7cb443f	416	3dca1312f6086a18893e37ffa246e515	Myc_reduce_mice_liver_24m_v4
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	a7213731b133effec506851ef7cb443f	615	1e2b12ca47f7ae90387a2aabf7bce2cf	Myc_reduce_mice_liver_24m_v1

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"
)

# 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
  )
}
#> Removing signature_id = '615' from collection_id = '462' completed.

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"
)

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

collection_id	collection_name	description	user_name	date_created	collection_hashkey	signature_id	signature_collection_hashkey	signature_name
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	a7213731b133effec506851ef7cb443f	414	dcb983859cddb392e870425335dc5b51	Myc_reduce_mice_liver_24m_v2
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	a7213731b133effec506851ef7cb443f	415	84b1e6d75210adac4c113f5fd0f66324	Myc_reduce_mice_liver_24m_v3
462	my_collection	This is the updated description.	montilab	2026-01-27 16:03:43	a7213731b133effec506851ef7cb443f	416	3dca1312f6086a18893e37ffa246e515	Myc_reduce_mice_liver_24m_v4

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"
)

# 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
  )
}
#> Remove collection_id = '462' from 'collection' table of the database.
#> Remove collection_id = '462' from 'collection_access' table of the database.
#> Remove signatures belongs to collection_id = '462' from 'signature_collection_access' table of the database.
#> collection_id = '462' has been removed.

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"`