Compare your list of microbes with published microbial signatures from BugSigDB or phenotypic annotation sets from BugPhyzz. The app calculates similarity metrics, including the Jaccard Index and Overlap Coefficient, to identify shared taxa between sets.

Getting Started

Follow these steps to try the app:

  1. Load an example: Click the "ncbi" link below the text box to load a sample list of bacteria.
  2. Use default settings: Leave all options at their default values.
  3. Run the analysis: Click the "Analyze" button in the Actions section.

For more details, check the help documentation.

Input

Load example text:
ncbi
taxname
metaphlan

Download example files:

Database options

Analysis options

Actions

Download result

About

The BugSigDBEnrich app allows the comparison of a list of microbes with BugSigDB, a manually curated database of microbial signatures from published studies. It also enables comparisons with Bugphyzz, which provides annotations of physiological and other phenotypic bacterial traits.

Package/app DESCRIPTION file:

Package: BugSigDBEnrich
Type: Package
Title: A shiny app for BugSigDB
Version: 0.99.27
Authors@R: 
    c(
        person(
            given = "Samuel", family = "Gamboa", role = c("aut", "cre"),
            email = "samuel.gamboa.tuz@gmail.com",
            comment = c(ORCID = "0000-0002-6863-7943")
        ),
        person(
            given = "Levi", family = "Waldron", role = c("aut"),
            comment = c(ORCID = "0000-0003-2725-0694")
        )
    )
Description: 
    The BugSigDBEnrich app allows the comparison of a list of microbes with
    BugSigDB, a manually curated database of microbial signatures from published
    studies. It also enables comparisons with Bugphyzz, which provides
    annotations of physiological and other phenotipic bacterial traits.
License: Artistic-2.0
Encoding: UTF-8
Imports: bsicons, bslib, bugphyzz, bugsigdbr, BugSigDBStats,
        cacheTaxonomizr, dplyr, DT, htmltools, htmlwidgets,
        ontologySimilarity, purrr, rlang, shiny, shinythemes,
        shinyWidgets, stringr, taxonomizr, tools, utils, waiter
Remotes: sdgamboa/cacheTaxonomizr@devel, waldronlab/BugSigDBStats@main
RoxygenNote: 7.3.2
URL: https://github.com/waldronlab/BugSigDBEnrich
BugReports: https://github.com/waldronlab/BugSigDBEnrich/issues
Depends: R (>= 4.4)
RemoteType: github
RemoteHost: api.github.com
RemoteRepo: BugSigDBEnrich
RemoteUsername: waldronlab
RemoteRef: HEAD
RemoteSha: 865667e34c249c6b1f26aba3bba2feaef61e5cb1
GithubRepo: BugSigDBEnrich
GithubUsername: waldronlab
GithubRef: HEAD
GithubSHA1: 865667e34c249c6b1f26aba3bba2feaef61e5cb1
NeedsCompilation: no
Packaged: 2024-12-20 22:10:58 UTC; samuelgamboa
Author: Samuel Gamboa [aut, cre] (<https://orcid.org/0000-0002-6863-7943>),
  Levi Waldron [aut] (<https://orcid.org/0000-0003-2725-0694>)
Maintainer: Samuel Gamboa <samuel.gamboa.tuz@gmail.com>
Built: R 4.4.2; ; 2024-12-20 22:10:59 UTC; unix
Find help about this app here.

Run locally

If you prefer to run this app locally, install the BugSiGDBEnrich package on your machine and launch the app directly from R.

  • Install package:
BiocManager::install("waldronlab/BugSigDBEnrich", dependencies = TRUE)
  • Run the app:
BugSigDBEnrich::BugSigDBEnrich()

Report a Bug

Please report bugs here.