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Package: ubigen
Title: Graphical Interface for Finding Patterns in Gene Expression
Version: 0.0.0.9000
Authors@R:
person(
"Elias",
"Projahn",
email = "elias@johrpan.de",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-4153-4071")
)
Description: This package contains precomputed data including comparisons in
gene expression. It provides a graphical interface to analyze and visualize
those data.
License: AGPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Depends:
R (>= 2.10)
LazyData: true
Imports:
bslib,
data.table,
DT,
glue,
shiny

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GNU Affero General Public License
=================================
_Version 3, 19 November 2007_
_Copyright (C) 2007 Free Software Foundation, Inc. &lt;<https://fsf.org/>&gt;_
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.
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### 8. Termination.
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### 11. Patents.
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### 12. No Surrender of Others' Freedom.
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### 13. Remote Network Interaction; Use with the GNU General Public License.
Notwithstanding any other provision of this License, if you modify the
Program, your modified version must prominently offer all users
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### 14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions
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If the Program specifies that a proxy can decide which future versions
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Later license versions may give you additional or different
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### 15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT
WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
CORRECTION.
### 16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR
LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER
PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
### 17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
## How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these
terms.
To do so, attach the following notices to the program. It is safest to
attach them to the start of each source file to most effectively state
the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper
mail.
If your software can interact with users remotely through a computer
network, you should also make sure that it provides a way for users to
get its source. For example, if your program is a web application, its
interface could display a "Source" link that leads users to an archive
of the code. There are many ways you could offer source, and different
solutions will be better for different programs; see section 13 for
the specific requirements.
You should also get your employer (if you work as a programmer) or
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. For more information on this, and how to apply and follow
the GNU AGPL, see <https://www.gnu.org/licenses/>.

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# Generated by roxygen2: do not edit by hand
export(run_app)
import(shiny)
importFrom(data.table,":=")
importFrom(data.table,.BY)
importFrom(data.table,.EACHI)
importFrom(data.table,.GRP)
importFrom(data.table,.I)
importFrom(data.table,.N)
importFrom(data.table,.NGRP)
importFrom(data.table,.SD)
importFrom(data.table,data.table)

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#' Run the application server.
#'
#' @param port The port to serve the application on.
#'
#' @export
run_app <- function(port = 3464) {
runApp(shinyApp(ui, server), port = port)
}

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#' A `data.table` containig data on genes and their expression behavior.
"genes"

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#' Server implementing the main user interface.
#' @noRd
server <- function(input, output) {
output$all_data <- DT::renderDataTable({
data <- ubigen::genes[, .(
"Gene" = glue::glue_data(
ubigen::genes,
"<a href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary",
"?db=core;g={gene}\" target=\"_blank\">{hgnc_name}</a>"
),
"Rank" = rank,
"Score" = score,
"Median" = median_expression,
"Mean" = mean_expression,
"Standard deviation" = sd_expression,
"Expressed" = above_zero,
"Above 50 TPM" = above_threshold,
"Above median" = above_median,
"Above 95%" = above_95
)]
DT::datatable(
data,
options = list(pageLength = 100),
rownames = FALSE,
escape = FALSE
) |>
DT::formatPercentage(c(
"Score",
"Expressed",
"Above 50 TPM",
"Above median",
"Above 95%"
)) |>
DT::formatRound(c(
"Median",
"Mean",
"Standard deviation"
))
})
}

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#' Function for creating the main user interface.
#' @noRd
ui <- function() {
navbarPage(
theme = bslib::bs_theme(
version = 5,
bootswatch = "united",
primary = "#7d19bf"
),
title = "Ubigen",
tabPanel(
"Explore",
sidebarLayout(
sidebarPanel(
width = 3,
),
mainPanel(
width = 9,
)
)
),
tabPanel(
title = "Data",
DT::dataTableOutput("all_data")
),
tabPanel(
title = "Publication"
)
)
}

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#' Various things that should be imported into the package namespace.
#'
#' @importFrom data.table :=
#' @importFrom data.table .BY
#' @importFrom data.table .EACHI
#' @importFrom data.table .GRP
#' @importFrom data.table .I
#' @importFrom data.table .N
#' @importFrom data.table .NGRP
#' @importFrom data.table .SD
#' @importFrom data.table data.table
#'
#' @import shiny
NULL

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{genes}
\alias{genes}
\title{A \code{data.table} containig data on genes and their expression behavior.}
\format{
An object of class \code{data.table} (inherits from \code{data.frame}) with 56156 rows and 13 columns.
}
\usage{
genes
}
\description{
A \code{data.table} containig data on genes and their expression behavior.
}
\keyword{datasets}

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/app.R
\name{run_app}
\alias{run_app}
\title{Run the application server.}
\usage{
run_app(port = 3464)
}
\arguments{
\item{port}{The port to serve the application on.}
}
\description{
Run the application server.
}