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SigRepo: An R package for storing and processing omic signatures

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The SigRepo package provides a comprehensive set of functions for easy storage and management of biological signatures and their components. SigRepo (the client) works alongside SigRepo_Server, its server counterpart. While SigRepo enables you to store, search, and retrieve signatures and signature collections, these operations rely on a running SigRepo_Server instance.

Interested in setting up your own SigRepo_Server? Check out the installation instructions here.

To upload and download signatures — and to fully utilize the functionalities offered by the SigRepo package — signatures and signature collections must be represented as specific R6 objects. You can create these objects using our proprietary package, OmicSignature.

Click on each link below for more information:

Below, we walk you through few essential steps to install the SigRepo package, and to store, retrieve, and interact with a list of signatures stored in an already deployed SigRepo server.

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 tidyverse package
library(tidyverse)

# Load SigRepo package
library(SigRepo)

# Load OmicSignature package
library(OmicSignature)

Before you begin

Please navigate to our sigrepo.org portal to create your account. On the login page, click "Register here!" and fill out the registration form to create an account. You will receive an email when your account has been activated. Due to SQL constraints, having multiple users on the same testing account, like running the tutorial in the readme, will fail to connect. Each user using their own account is ideal.

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 SigRepo::newConnHandler() function to create a handler which contains user credentials to establish connection to our 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 provide two signature objects that comes with the package for demonstrations:

  1. LLFS_Aging_Gene_2023
  2. Myc_reduce_mice_liver_24m

Upload a signature

The SigRepo::addSignature() function allows users to upload a signature to the database.

IMPORTANT NOTE:

  • User MUST HAVE an editor or admin account to use this function.
  • A signature MUST BE an R6 object obtained from OmicSignature::OmicSignature()

Example 1: Upload LLFS_Aging_Gene_2023 signature

## Show the OmicSignature summary
print(LLFS_Aging_Gene_2023)
#> Signature Object: 
#>   Metadata: 
#>     adj_p_cutoff = 0.01 
#>     assay_type = transcriptomics 
#>     covariates = sex,fc,education,percent_intergenic,PC1-4,GRM 
#>     direction_type = bi-directional 
#>     keywords = human, aging, LLFS 
#>     organism = Homo Sapiens 
#>     phenotype = Aging 
#>     platform = transcriptomics by array 
#>     sample_type = blood 
#>     score_cutoff = 6 
#>     signature_name = LLFS_Aging_Gene_2023 
#>     year = 2023 
#>   Signature: 
#>     Group1 (82)
#>     Group2 (87)
#>   Differential Expression Data: 
#>     1000 x 8

## Add the signature to the repository
SigRepo::addSignature(
  conn_handler = conn_handler, 
  omic_signature = LLFS_Aging_Gene_2023
)
#> Uploading signature metadata to the database...
#> Saving difexp to the database...
#> now dyn.load("/Library/Frameworks/R.framework/Versions/4.5-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: 489

Example 2: Upload Myc_reduce_mice_liver_24m signature

In this example, we show what happens when the OmicSignature contains feature_name’s that are not part of “dictionary” for the corresponding omics layer.

## Show the OmicSignature summary
print(Myc_reduce_mice_liver_24m)
#> Signature Object: 
#>   Metadata: 
#>     adj_p_cutoff = 0.05 
#>     assay_type = transcriptomics 
#>     covariates = none 
#>     description = mice Myc haploinsufficient (Myc(+/-)) 
#>     direction_type = bi-directional 
#>     keywords = Myc, KO, longevity 
#>     organism = Mus musculus 
#>     others = C57BL/6 
#>     phenotype = Myc_reduce 
#>     platform = transcriptomics by array 
#>     PMID = 25619689 
#>     sample_type = liver 
#>     score_cutoff = 5 
#>     signature_name = Myc_reduce_mice_liver_24m 
#>     year = 2015 
#>   Metadata user defined fields: 
#>     animal_strain = C57BL/6 
#>   Signature: 
#>     Group1 (30)
#>     Group2 (78)
#>   Differential Expression Data: 
#>     1000 x 5

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.

Example 3: 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 = "Myc, KO, longevity",
  cutoff_description = NULL,
  author = NULL,
  PMID = "25619689",
  year = 2015,

  # example of customized attributes:
  others = base::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...
#> 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: 491

Search for a list of signatures

The SigRepo::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.

# Get all signatures
signature_tbl <- SigRepo::searchSignature(conn_handler = conn_handler)

# WARNINGS: THE SIGNATURE TABLE CAN BE LARGE, SO ONLY THE FIRST SIX OBSERVATIONS ARE SHOWN.
if(base::nrow(signature_tbl) > 0){
  knitr::kable(
    utils::head(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
213 Aging_Hs_HNSC_RNASeq_TCGA_ACC_MontiLab2025 Homo sapiens bi-directional transcriptomics Aging transcriptomics by bulk RNA-seq unknown tumor purity, race, gender TCGA HPV-negative ACC aging signature 0 NA NA 1 NA TCGA,ACC,Aging NA 2025 NA 1 32402 18031 14371 H_Nikoueian 2025-10-03 15:01:24 0 37b8bb25907349dfaa1b38fecc9e872b
214 Aging_Hs_HNSC_RNASeq_TCGA_BLCA_MontiLab2025 Homo sapiens bi-directional transcriptomics Aging transcriptomics by bulk RNA-seq unknown tumor purity, race, gender TCGA HPV-negative BLCA aging signature 0 NA NA 1 NA TCGA,BLCA,Aging NA 2025 NA 1 39689 22346 17343 H_Nikoueian 2025-10-03 15:01:35 0 28d8ba3d012ecbc6a080996fc2dcd66e
215 Aging_Hs_HNSC_RNASeq_TCGA_BRCA_MontiLab2025 Homo sapiens bi-directional transcriptomics Aging transcriptomics by bulk RNA-seq unknown tumor purity, race, gender TCGA HPV-negative BRCA aging signature 0 NA NA 1 NA TCGA,BRCA,Aging NA 2025 NA 1 42011 26478 15533 H_Nikoueian 2025-10-03 15:01:49 0 9ae65c31c82b6edc15819fb7f8cd0640
216 Aging_Hs_HNSC_RNASeq_TCGA_CESC_MontiLab2025 Homo sapiens bi-directional transcriptomics Aging transcriptomics by bulk RNA-seq unknown tumor purity, race, gender TCGA HPV-negative CESC aging signature 0 NA NA 1 NA TCGA,CESC,Aging NA 2025 NA 1 38521 21746 16775 H_Nikoueian 2025-10-03 15:02:05 0 e487cfd606e3d4e2214a8e4435b424b8
217 Aging_Hs_HNSC_RNASeq_TCGA_COAD_MontiLab2025 Homo sapiens bi-directional transcriptomics Aging transcriptomics by bulk RNA-seq unknown tumor purity, race, gender TCGA HPV-negative COAD aging signature 0 NA NA 1 NA TCGA,COAD,Aging NA 2025 NA 1 38857 22186 16671 H_Nikoueian 2025-10-03 15:02:20 0 afb09a078a63c9342530d2a119698085
218 Aging_Hs_HNSC_RNASeq_TCGA_ESCA_MontiLab2025 Homo sapiens bi-directional transcriptomics Aging transcriptomics by bulk RNA-seq unknown tumor purity, race, gender TCGA HPV-negative ESCA aging signature 0 NA NA 1 NA TCGA,ESCA,Aging NA 2025 NA 1 42053 15816 26237 H_Nikoueian 2025-10-03 15:02:33 0 3275eeda945640a32d963a55d22143a9

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(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
489 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 montilab 2025-10-18 02:37:13 0 b35b7c1d387440d474bfcb3cb162c9a6

Retrieve a list of omic signatures

The SigRepo::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 PRIVATE and belongs to other user in the database, users will need to be given an editor permission 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

# WARNINGS: THE SIGNATURE LIST CAN BE LARGE TO DOWNLOAD (NOT RUN)
signature_list <- SigRepo::getSignature(conn_handler = conn_handler)

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 SigRepo::deleteSignature() function allows users to delete a signature from the database.

IMPORTANT NOTE:

  • Users MUST HAVE an editor or admin account to use this function.
  • Users can ONLY DELETE their own uploaded signatures or were given an editor permission 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(base::nrow(signature_tbl) > 0){
  SigRepo::deleteSignature(
    conn_handler = conn_handler, 
    signature_id = signature_tbl$signature_id  
  )
}
#> Remove difexp belongs to signature_id = '489' from the database.
#> Remove signature_id = '489' from 'signatures' table of the database.
#> Remove features belongs to signature_id = '489' from 'signature_feature_set' table of the database.
#> Remove user access to signature_id = '489' from 'signature_access' table of the database.
#> Remove signature_id = '489' from 'signature_collection_access' table of the database.
#> signature_id = '489' has been removed.

Update a signature

The SigRepo::updateSignature() function allows users to update a specific signature in the SigRepo database.

IMPORTANT NOTE:

  • Users MUST HAVE an editor or admin account to use this function.
  • Users can ONLY UPDATE their own uploaded signatures or were given an editor permission 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 a correct value, e.g., platform = "transcriptomics by single-cell RNA-seq". You can use the SigRepo::updateSignature() function as follows:

# 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 = "Myc, KO, longevity",
  cutoff_description = NULL,
  author = NULL,
  PMID = "25619689",
  year = 2015,

  # example of customized attributes:
  others = base::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$score) > metadata_revised$score_cutoff & .data$adj_p < metadata_revised$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 = '491' 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
491 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 montilab 2025-10-18 02:37:41 0 a10176ce6e727366cf740e2bfb56e2bc

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(base::nrow(signature_tbl) > 0){
  SigRepo::deleteSignature(
    conn_handler = conn_handler, 
    signature_id = signature_tbl$signature_id
  )
}
#> Remove difexp belongs to signature_id = '491' from the database.
#> Remove signature_id = '491' from 'signatures' table of the database.
#> Remove features belongs to signature_id = '491' from 'signature_feature_set' table of the database.
#> Remove user access to signature_id = '491' from 'signature_access' table of the database.
#> Remove signature_id = '491' from 'signature_collection_access' table of the database.
#> signature_id = '491' has been removed.

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SigRepo: An R package for storing and processing omic signatures

montilab.github.io/SigRepo/

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First version of SigRepoR Latest
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