The SigRepo package includes a suite of functions for easily storing and managing biological signatures and its constituents. Currently, Sigrepo is capable of storing, searching, and retrieving signatures and its signature collections from a MySQL database of choice. Interest in setting-up your own SigRepo database? See here on how to initiate a MySQL database with the appropriate schema.
In order to interact with a suite of functions in SigRepo package, the input data must represent an R6 object for the representation of signatures and signature collections, and they can be created using our proprietary package, OmicSignature.
Click on each link below for more information:
- Overview of the object structure
- Create an OmicSignature (OmS)
- Create an OmicSignatureCollection (OmSC)
For demonstrations, we will walk through the steps of how to use SigRepo package to store, retrieve, and interact with a list of signatures stored in our MySQL SigRepo Database.
Installation
- Using
devtoolspackage
# Load devtools package
library(devtools)
# Install SigRepo
devtools::install_github(repo = 'montilab/SigRepo')
# Install OmicSignature
devtools::install_github(repo = 'montilab/OmicSignature')
# Load tidyverse package
library(tidyverse)
# Load SigRepo package
library(SigRepo)
# Load OmicSignature package
library(OmicSignature)Connect to SigRepo Database
We adopt a MySQL database structure for efficiently storing, searching, and retrieving the biological signatures and its constituents. To access the signatures stored in our database, VISIT OUR WEBSITE to create an account or CONTACT US to be added.
There are three types of user accounts:
- admin has READ and WRITE access to all signatures in the database.
- editor has READ and WRITE access to ONLY their own uploaded signatures in the database.
- viewer has ONLY READ access to see a list of signatures that are publicly available in the database but DO NOT HAVE WRITE access to the database.
Once you have a valid account, to connect to our SigRepo database, one can use the newConnHandler() function to create a handler which contains user credentials to establish connection to our database.
Load Signatures
Here, we provide two signature objects that comes with the package for demonstrations:
- LLFS_Aging_Gene_2023
- Myc_reduce_mice_liver_24m
Upload a signature
The addSignature() function allows users to upload a signature to the database.
IMPORTANT NOTE:
- User MUST HAVE an
editororadminaccount to use this function. - A signature MUST BE an R6 object obtained from OmicSignature::OmicSignature()
Example 1: Create an omic signature using OmicSignature package and upload to the database
# Create an OmicSignature metadata
metadata <- OmicSignature::createMetadata(
# required attributes:
signature_name = "Myc_reduce_mice_liver_24m_readme",
organism = "Mus musculus",
direction_type = "bi-directional",
assay_type = "transcriptomics",
phenotype = "Myc_reduce",
# optional and recommended:
covariates = "none",
description = "mice Myc haploinsufficient (Myc(+/-))",
platform = "transcriptomics by array",
sample_type = "liver", # use BRENDA ontology
# optional cut-off attributes.
# specifying them can facilitate the extraction of signatures.
logfc_cutoff = NULL,
p_value_cutoff = NULL,
adj_p_cutoff = 0.05,
score_cutoff = 5,
# other optional built-in attributes:
keywords = c("Myc", "KO", "longevity"),
cutoff_description = NULL,
author = NULL,
PMID = 25619689,
year = 2015,
# example of customized attributes:
others = list("animal_strain" = "C57BL/6")
)
# Create difexp object
difexp <- base::readRDS(base::file.path(base::system.file("extdata", package = "OmicSignature"), "difmatrix_Myc_mice_liver_24m.rds"))
base::colnames(difexp) <- OmicSignature::replaceDifexpCol(base::colnames(difexp))
#> Warning in OmicSignature::replaceDifexpCol(base::colnames(difexp)): Required
#> column for OmicSignature object difexp: feature_name, is not found in your
#> input. This may cause problem when creating your OmicSignature object.
# Rename ensembl with feature name and add group label to difexp
difexp <- difexp |>
dplyr::rename(feature_name = ensembl) |>
dplyr::mutate(group_label = base::as.factor(base::ifelse(.data$score > 0, "MYC Reduce", "WT")))
# Create signature object
signature <- difexp |>
dplyr::filter(base::abs(.data$score) > metadata$score_cutoff & .data$adj_p < metadata$adj_p_cutoff) |>
dplyr::select(c("probe_id", "feature_name", "score")) |>
dplyr::mutate(group_label = base::as.factor(base::ifelse(.data$score > 0, "MYC Reduce", "WT")))
# Create signature object
omic_signature <- OmicSignature::OmicSignature$new(
metadata = metadata,
signature = signature,
difexp = difexp
)
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_readme created.
# Add signature to database
SigRepo::addSignature(
conn_handler = conn_handler, # A handler contains user credentials to establish connection to a remote database
omic_signature = omic_signature, # An R6 object obtained from OmicSignature::OmicSignature()
visibility = FALSE, # Whether to make signature public or private. Default is FALSE.
return_signature_id = FALSE, # Whether to return the uploaded signature id. Default is FALSE.
verbose = TRUE # Whether to print diagnostic messages. Default is TRUE.
)
#> Uploading signature metadata to the database...
#> Saving difexp to the database...
#> now dyn.load("/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/curl/libs/curl.so") ...
#> Adding signature owner to the signature access table of the database...
#> Adding signature feature set to the database...
#> Finished uploading.
#> ID of the uploaded signature: 11
Example 2: Upload LLFS_Aging_Gene_2023 signature
SigRepo::addSignature(
conn_handler = conn_handler,
omic_signature = LLFS_Aging_Gene_2023
)
#> Uploading signature metadata to the database...
#> Saving difexp to the database...
#> Adding signature owner to the signature access table of the database...
#> Adding signature feature set to the database...
#> Finished uploading.
#> ID of the uploaded signature: 12
Example 3: Upload Myc_reduce_mice_liver_24m signature
missing_features <- SigRepo::addSignature(
conn_handler = conn_handler,
omic_signature = Myc_reduce_mice_liver_24m,
return_missing_features = TRUE # Whether to return a list of missing features during upload.
)
#> Uploading signature metadata to the database...
#> Saving difexp to the database...
#> Adding signature owner to the signature access table of the database...
#> Adding signature feature set to the database...
#> Warning in SigRepo::showTranscriptomicsErrorMessage(db_table_name = ref_table, :
#> The following features do not existed in the 'transcriptomics_features' table of the database:
#> 'ENSG00000213949'
#> 'ENSG00000127946'
#> 'ENSG00000159167'
#> 'ENSG00000111335'
#> 'ENSG00000033327'
#> 'ENSG00000266472'
#> 'ENSG00000088280'
#> 'ENSG00000074935'
#> 'ENSG00000205318'
#> 'ENSG00000145781'
#> 'ENSG00000182158'
#> 'ENSG00000275183'
#> 'ENSG00000137876'
#> 'ENSG00000135069'
#> 'ENSG00000108582'
#> 'ENSG00000165312'
#> 'ENSG00000135205'
#> 'ENSG00000151726'
#> 'ENSG00000197879'
#> 'ENSG00000154310'
#> 'ENSG00000116016'
#> 'ENSG00000082781'
#> 'ENSG00000141258'
#> 'ENSG00000107833'
#> 'ENSG00000102858'
#> 'ENSG00000182054'
#> 'ENSG00000167106'
#> 'ENSG00000100196'
#> 'ENSG00000150347'
#> 'ENSG00000123977'
#> 'ENSG00000143553'
#> 'ENSG00000182704'
#> 'ENSG00000134909'
#> 'ENSG00000139725'
#> 'ENSG00000170542'
#> 'ENSG00000041982'
#> 'ENSG00000162511'
#> 'ENSG00000134243'
#> 'ENSG00000095383'
#> 'ENSG00000198925'
#> 'ENSG00000163872'
#> 'ENSG00000180891'
#> 'ENSG00000126368'
#> 'ENSG00000014914'
#> 'ENSG00000186104'
#> 'ENSG00000109472'
#> 'ENSG00000196924'
#> 'ENSG00000100605'
#> 'ENSG00000113070'
#> 'ENSG00000145431'
#> 'ENSG00000167272'
#> 'ENSG00000100280'
#> 'ENSG00000182518'
#> 'ENSG00000155363'
#> 'ENSG00000213445'
#> 'ENSG00000272620'
#> 'ENSG00000179941'
#> 'ENSG00000108561'
#> 'ENSG00000005100'
#> 'ENSG00000117616'
#> 'ENSG00000161642'
#> 'ENSG00000196981'
#> 'ENSG00000125434'
#> 'ENSG00000140937'
#> 'ENSG00000105287'
#> 'ENSG00000080561'
#> 'ENSG00000163932'
#> 'ENSG00000106399'
#> 'ENSG00000085185'
#> 'ENSG00000171298'
#> 'ENSG00000120333'
#> 'ENSG00000111875'
#> 'ENSG00000165507'
#> 'ENSG00000166797'
#> 'ENSG00000103404'
#> 'ENSG00000268043'
#> 'ENSG00000265972'
#> 'ENSG00000137494'
#> 'ENSG00000107485'
#> 'ENSG00000106397'
#> 'ENSG00000252623'
#> 'ENSG00000177084'
#> 'ENSG00000155189'
#> 'ENSG00000205189'
#> 'ENSG00000000419'
#> 'ENSG00000168275'
#> 'ENSG00000144674'
#> 'ENSG00000107263'
#> 'ENSG00000113083'
#> 'ENSG00000198873'
#> 'ENSG00000164347'
#> 'ENSG00000065526'
#> 'ENSG00000153294'
#> 'ENSG00000226742'
#> 'ENSG00000163617'
#> 'ENSG00000070047'
#> 'ENSG00000134330'
#> 'ENSG00000201962'
#> 'ENSG00000168538'
#> 'ENSG00000158042'
#> 'ENSG00000160072'
#> 'ENSG00000181634'
#> 'ENSG00000145022'
#> 'ENSG00000128510'
#> 'ENSG00000125037'
#> 'ENSG00000238357'
#> 'ENSG00000077157'
#> 'ENSG00000185989'
#>
#> You can use 'searchTranscriptomicsFeatureSet()' to see a list of available features.
#>
#> To add these features to our database, please contact our admin for support.Search for a list of signatures
The searchSignature() function allows users to search for all or a specific set of signatures that are available in the database.
Example 1: Search for all signatures
signature_tbl <- SigRepo::searchSignature(conn_handler = conn_handler)
if(nrow(signature_tbl) > 0){
knitr::kable(
signature_tbl,
row.names = FALSE
)
}| signature_id | signature_name | organism | direction_type | assay_type | phenotype | platform_name | sample_type | covariates | description | score_cutoff | logfc_cutoff | p_value_cutoff | adj_p_cutoff | cutoff_description | keywords | PMID | year | others | has_difexp | num_of_difexp | num_up_regulated | num_down_regulated | user_name | date_created | visibility | signature_hashkey |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 7 | Myc_reduce_mice_liver_24m_v1 | Mus musculus | bi-directional | transcriptomics | Myc_reduce | transcriptomics by array | liver | none | mice Myc haploinsufficient (Myc(+/-)) | 5 | NA | NA | 0.05 | NA | Myc,KO,longevity | 25619689 | 2015 | animal_strain: <C57BL/6> | 1 | 884 | 5 | 10 | root | 2025-09-19 19:50:04 | 0 | eacd0935d97847d56cb717455b0e48a3 |
| 8 | Myc_reduce_mice_liver_24m_v2 | Mus musculus | bi-directional | transcriptomics | Myc_reduce | transcriptomics by array | liver | none | mice Myc haploinsufficient (Myc(+/-)) | 5 | NA | NA | 0.05 | NA | Myc,KO,longevity | 25619689 | 2015 | animal_strain: <C57BL/6> | 1 | 884 | 5 | 10 | root | 2025-09-19 19:50:04 | 0 | ec356cabc33fcc22f8a0b77b24db91ab |
| 9 | Myc_reduce_mice_liver_24m_v3 | Mus musculus | bi-directional | transcriptomics | Myc_reduce | transcriptomics by array | liver | none | mice Myc haploinsufficient (Myc(+/-)) | 5 | NA | NA | 0.05 | NA | Myc,KO,longevity | 25619689 | 2015 | animal_strain: <C57BL/6> | 1 | 884 | 5 | 10 | root | 2025-09-19 19:50:07 | 0 | fa416468cc91f872f073e15efdaf1ece |
| 10 | Myc_reduce_mice_liver_24m_v4 | Mus musculus | bi-directional | transcriptomics | Myc_reduce | transcriptomics by array | liver | none | mice Myc haploinsufficient (Myc(+/-)) | 5 | NA | NA | 0.05 | NA | Myc,KO,longevity | 25619689 | 2015 | animal_strain: <C57BL/6> | 1 | 884 | 5 | 10 | root | 2025-09-19 19:50:07 | 0 | 5bc419a0fbd2c012e669a19c67f2b434 |
| 11 | Myc_reduce_mice_liver_24m_readme | Mus musculus | bi-directional | transcriptomics | Myc_reduce | transcriptomics by array | liver | none | mice Myc haploinsufficient (Myc(+/-)) | 5 | NA | NA | 0.05 | NA | Myc,KO,longevity | 25619689 | 2015 | animal_strain: <C57BL/6> | 1 | 884 | 5 | 10 | root | 2025-09-24 13:06:55 | 0 | 7e24a413c1287f840d492b2963c263a5 |
| 12 | LLFS_Aging_Gene_2023 | Homo sapiens | bi-directional | transcriptomics | Aging | transcriptomics by array | blood | sex,fc,education,percent_intergenic,PC1-4,GRM | NA | 6 | NA | NA | 0.01 | NA | human,aging,LLFS | NA | 2023 | NA | 1 | 1000 | 82 | 87 | root | 2025-09-24 13:06:56 | 0 | 7fdecac66691beed1703efc25487768c |
Example 2: Search for a specific signature, e.g., signature_name = “LLFS_Aging_Gene_2023”
signature_tbl <- SigRepo::searchSignature(
conn_handler = conn_handler,
signature_name = "LLFS_Aging_Gene_2023"
)
if(nrow(signature_tbl) > 0){
knitr::kable(
signature_tbl,
row.names = FALSE
)
}| signature_id | signature_name | organism | direction_type | assay_type | phenotype | platform_name | sample_type | covariates | description | score_cutoff | logfc_cutoff | p_value_cutoff | adj_p_cutoff | cutoff_description | keywords | PMID | year | others | has_difexp | num_of_difexp | num_up_regulated | num_down_regulated | user_name | date_created | visibility | signature_hashkey |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 12 | LLFS_Aging_Gene_2023 | Homo sapiens | bi-directional | transcriptomics | Aging | transcriptomics by array | blood | sex,fc,education,percent_intergenic,PC1-4,GRM | NA | 6 | NA | NA | 0.01 | NA | human,aging,LLFS | NA | 2023 | NA | 1 | 1000 | 82 | 87 | root | 2025-09-24 13:06:56 | 0 | 7fdecac66691beed1703efc25487768c |
Retrieve a list of omic signatures
The getSignature() function allows users to retrieve a list of omic signature objects that they are PUBLICLY available in the database.
IMPORTANT NOTE:
- Users can ONLY RETRIEVE a list of signatures that are publicly available in the database including their own uploaded signatures.
- If a signature is
PRIVATEand belongs to other user in the database, users will need to be given aneditorpermission from its owner in order to access, retrieve, and edit their signatures.
Example 1: Retrieve all signatures that are publicly available or owned by the user in the database
signature_list <- SigRepo::getSignature(conn_handler = conn_handler)
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_v1 created.
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_v2 created.
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_v3 created.
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_v4 created.
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_readme created.
#> [Success] OmicSignature object LLFS_Aging_Gene_2023 created.Example 2: Retrieve a specific signature that is publicly available or owned by the user in the database, e.g., signature_name = “LLFS_Aging_Gene_2023”
LLFS_oms <- SigRepo::getSignature(
conn_handler = conn_handler,
signature_name = "LLFS_Aging_Gene_2023"
)
#> [Success] OmicSignature object LLFS_Aging_Gene_2023 created.Delete a signature
The deleteSignature() function allows users to delete a signature from the database.
IMPORTANT NOTE:
- Users MUST HAVE an
editororadminaccount to use this function. - Users can ONLY DELETE their own uploaded signatures or were given an
editorpermission from its owner to access, retrieve, and edit their signatures. - Users can ONLY DELETE a signature one at a time.
For example: You want to remove signature_name = “LLFS_Aging_Gene_2023” from the database.
# Let's search for signature_name = "LLFS_Aging_Gene_2023" in the database
signature_tbl <- SigRepo::searchSignature(
conn_handler = conn_handler,
signature_name = "LLFS_Aging_Gene_2023"
)
# If the signature exists, remove it from the database
if(nrow(signature_tbl) > 0){
SigRepo::deleteSignature(
conn_handler = conn_handler,
signature_id = signature_tbl$signature_id
)
}
#> Remove difexp belongs to signature_id = '12' from the database.
#> Remove signature_id = '12' from 'signatures' table of the database.
#> Remove features belongs to signature_id = '12' from 'signature_feature_set' table of the database.
#> Remove user access to signature_id = '12' from 'signature_access' table of the database.
#> Remove signature_id = '12' from 'signature_collection_access' table of the database.
#> signature_id = '12' has been removed.Update a signature
The updateSignature() function allows users to update a specific signature in the SigRepo database.
IMPORTANT NOTE:
- Users MUST HAVE an
editororadminaccount to use this function. - Users can ONLY UPDATE their own uploaded signatures or were given an
editorpermission from its owner to access, retrieve, and edit their signatures. - Users can ONLY UPDATE a signature one at a time.
For example: If the platform information in the previous uploaded signature, “Myc_reduce_mice_liver_24m_readme”, is incorrect, and you wish to update the platform information with the correct value, e.g., platform = “transcriptomics by single-cell RNA-seq”. You can use the updateSignature() function as follows:
# 1. Revise the metadata object with new platform = transcriptomics by single-cell RNA-seq
metadata_revised <- OmicSignature::createMetadata(
# required attributes:
signature_name = "Myc_reduce_mice_liver_24m_readme",
organism = "Mus musculus",
direction_type = "bi-directional",
assay_type = "transcriptomics",
phenotype = "Myc_reduce",
# optional and recommended:
covariates = "none",
description = "mice Myc haploinsufficient (Myc(+/-))",
platform = "transcriptomics by single-cell RNA-seq",
sample_type = "liver", # use BRENDA ontology
# optional cut-off attributes.
# specifying them can facilitate the extraction of signatures.
logfc_cutoff = NULL,
p_value_cutoff = NULL,
adj_p_cutoff = 0.05,
score_cutoff = 5,
# other optional built-in attributes:
keywords = c("Myc", "KO", "longevity"),
cutoff_description = NULL,
author = NULL,
PMID = 25619689,
year = 2015,
# example of customized attributes:
others = list("animal_strain" = "C57BL/6")
)
# Create difexp object
difexp <- base::readRDS(base::file.path(base::system.file("extdata", package = "OmicSignature"), "difmatrix_Myc_mice_liver_24m.rds"))
base::colnames(difexp) <- OmicSignature::replaceDifexpCol(base::colnames(difexp))
#> Warning in OmicSignature::replaceDifexpCol(base::colnames(difexp)): Required
#> column for OmicSignature object difexp: feature_name, is not found in your
#> input. This may cause problem when creating your OmicSignature object.
# Rename ensembl with feature name and add group label to difexp
difexp <- difexp |>
dplyr::rename(feature_name = ensembl) |>
dplyr::mutate(group_label = base::as.factor(base::ifelse(.data$score > 0, "MYC Reduce", "WT")))
# Create signature object
signature <- difexp |>
dplyr::filter(base::abs(.data$score) > metadata$score_cutoff & .data$adj_p < metadata$adj_p_cutoff) |>
dplyr::select(c("probe_id", "feature_name", "score")) |>
dplyr::mutate(group_label = base::as.factor(base::ifelse(.data$score > 0, "MYC Reduce", "WT")))
# Create signature object
updated_omic_signature <- OmicSignature::OmicSignature$new(
metadata = metadata_revised,
signature = signature,
difexp = difexp
)
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_readme created.
# Now, let's search for Myc_reduce_mice_liver_24m_readme in the database
# in which we would like to revise the value of platform to 'transcriptomics by single-cell RNA-seq'
signature_tbl <- SigRepo::searchSignature(
conn_handler = conn_handler,
signature_name = metadata_revised$signature_name
)
# If signature exists, update the signature with the revised omic_signature object
if(base::nrow(signature_tbl) > 0){
SigRepo::updateSignature(
conn_handler = conn_handler,
signature_id = signature_tbl$signature_id,
omic_signature = updated_omic_signature
)
}
#> [Success] OmicSignature object Myc_reduce_mice_liver_24m_readme created.
#> signature_id = '11' has been updated.Let’s look up signature_name = “Myc_reduce_mice_liver_24m_readme” and see if the value of platform has been changed.
signature_tbl <- SigRepo::searchSignature(
conn_handler = conn_handler,
signature_name = "Myc_reduce_mice_liver_24m_readme"
)
if(base::nrow(signature_tbl) > 0){
knitr::kable(
signature_tbl,
row.names = FALSE
)
}| signature_id | signature_name | organism | direction_type | assay_type | phenotype | platform_name | sample_type | covariates | description | score_cutoff | logfc_cutoff | p_value_cutoff | adj_p_cutoff | cutoff_description | keywords | PMID | year | others | has_difexp | num_of_difexp | num_up_regulated | num_down_regulated | user_name | date_created | visibility | signature_hashkey |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 11 | Myc_reduce_mice_liver_24m_readme | Mus musculus | bi-directional | transcriptomics | Myc_reduce | transcriptomics by single-cell RNA-seq | liver | none | mice Myc haploinsufficient (Myc(+/-)) | 5 | NA | NA | 0.05 | NA | Myc,KO,longevity | 25619689 | 2015 | animal_strain: <C57BL/6> | 1 | 884 | 5 | 10 | root | 2025-09-24 13:07:00 | 0 | 7e24a413c1287f840d492b2963c263a5 |
Finally, remove signature_name = “Myc_reduce_mice_liver_24m_readme” from the database
# Let's search for signature_name = "Myc_reduce_mice_liver_24m_readme" in the database
signature_tbl <- SigRepo::searchSignature(
conn_handler = conn_handler,
signature_name = "Myc_reduce_mice_liver_24m_readme"
)
# If the signature exists, remove it from the database
if(nrow(signature_tbl) > 0){
SigRepo::deleteSignature(
conn_handler = conn_handler,
signature_id = signature_tbl$signature_id
)
}
#> Remove difexp belongs to signature_id = '11' from the database.
#> Remove signature_id = '11' from 'signatures' table of the database.
#> Remove features belongs to signature_id = '11' from 'signature_feature_set' table of the database.
#> Remove user access to signature_id = '11' from 'signature_access' table of the database.
#> Remove signature_id = '11' from 'signature_collection_access' table of the database.
#> signature_id = '11' has been removed.