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‎.Rbuildignore

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^reTCR\.Rproj$
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^\.Rproj\.user$
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^LICENSE\.md$

‎.gitignore

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.Rproj.user
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.Rhistory
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.Rdata
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.httr-oauth
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.DS_Store
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.quarto

‎DESCRIPTION

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Package: reTCR
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Title: TCR Repertoire Analysis in R
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Version: 0.0.0.9000
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Authors@R:
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c(
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person("Abdullah", "Al Nahid", email= "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4390-0768")),
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person("Karishma", "Chhugani", email = "[email protected]", role = c("aut"), comment = c(ORCID = "")),
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person("Ella Maria", "Schwab", email = "[email protected]", role = c("aut"), comment = c(ORCID = "")),
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person("Serghei", "Mangul", email = "[email protected]", role = c("aut", "rev"), comment = c(ORCID = "")),
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)
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Description: The reTCR R package offers a streamlined framework for processing and analyzing TCR repertoire data from high-throughput sequencing experiments. It leverages the MiXCR software with custom presets tailored to different library preparation methods, ensuring standardized data processing for comparative studies. The package integrates seamlessly with R, enabling researchers to query and filter TCR repertoire data based on various metadata characteristics such as disease phenotype, age, gender, and library preparation methods. Additionally, it incorporates the pyTCR tool, which calculates a comprehensive set of diversity metrics, including the Shannon-Wiener index, Gini coefficient, weighted usage of V, D, and J genes, and the mean length of CDR3 nucleotide sequences, providing a robust platform for in-depth immune repertoire analysis.
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License: MIT + file LICENSE
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.2.3
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Suggests:
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testthat (>= 3.0.0)
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Config/testthat/edition: 3

‎LICENSE

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YEAR: 2024
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COPYRIGHT HOLDER: Mangul Lab

‎LICENSE.md

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# MIT License
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Copyright (c) 2024 Mangul Lab
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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‎NEWS.md

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# reTCR (development version)
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* Initial CRAN submission.

‎README.md

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# reTCR
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<!-- badges: start -->
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<!-- badges: end -->
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The goal of reTCR is to ...
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## Installation
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You can install the development version of reTCR like so:
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``` r
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# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?
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```
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## Example
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This is a basic example which shows you how to solve a common problem:
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``` r
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library(reTCR)
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## basic example code
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```
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‎reTCR.Rproj

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Version: 1.0
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RestoreWorkspace: No
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SaveWorkspace: No
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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LineEndingConversion: Posix
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source
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PackageRoxygenize: rd,collate,namespace

‎tests/testthat.R

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# This file is part of the standard setup for testthat.
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# It is recommended that you do not modify it.
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#
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# Where should you do additional test configuration?
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# Learn more about the roles of various files in:
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# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
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# * https://testthat.r-lib.org/articles/special-files.html
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library(testthat)
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library(reTCR)
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test_check("reTCR")

‎tests/testthat/test-my-test.R

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test_that("multiplication works", {
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expect_equal(2 * 2, 4)
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})

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