diff --git a/.Rbuildignore b/.Rbuildignore index 8fbbb90..4e88465 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -9,3 +9,4 @@ ^dev$ ^\.positai$ ^\.claude$ +^LICENSE\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index f6ebd4b..0c9b05b 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Authors@R: person("Timothy", "Sundell", , "timothy.sundell@gu.se", role = c("aut", "cre"), comment = c(ORCID = "https://orcid.org/0000-0001-6244-1790")) Description: A collection of functions from TS, for TS. -License: `use_mit_license()` +License: MIT + file LICENSE URL: https://timothysundell.github.io/TS/ Depends: R (>= 2.10) @@ -36,4 +36,4 @@ Imports: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 +Config/roxygen2/version: 8.0.0 diff --git a/LICENSE b/LICENSE index ba16401..a59f7be 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,2 @@ -MIT License - -Copyright (c) 2023 Timothy Sundell - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +YEAR: 2026 +COPYRIGHT HOLDER: Timothy Sundell diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..2487a33 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,21 @@ +# MIT License + +Copyright (c) 2026 Timothy Sundell + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/NAMESPACE b/NAMESPACE index ce3f795..9c729e8 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -19,6 +19,7 @@ export(TS_extract_ranked_genes_per_PC) export(TS_featureplots) export(TS_find_cellranger_samples) export(TS_format_IMGT_to_cellranger) +export(TS_plan_cellranger_file_collection) export(TS_plot_3D) export(TS_plot_IG_usage) export(TS_plot_IG_usage_legacy) @@ -27,7 +28,6 @@ export(TS_plot_column_pattern_chart) export(TS_plot_counts_boxplot) export(TS_plot_counts_violin) export(TS_plot_enrichR) -export(TS_plan_cellranger_file_collection) export(TS_project_scRNAseq_dataset) export(TS_project_scRNAseq_dataset_export_query) export(TS_run_enrichR) diff --git a/man/TS_run_enrichR.Rd b/man/TS_run_enrichR.Rd index 4c1aab6..105e2b5 100644 --- a/man/TS_run_enrichR.Rd +++ b/man/TS_run_enrichR.Rd @@ -15,7 +15,7 @@ TS_run_enrichR( \arguments{ \item{gene_list}{Character vector containing genes to test} -\item{plot_enrichr}{Whether to plot the output using the enrichR function \link[enrichR:plotEnrich]{enrichR::plotEnrich}. Defaults to 'FALSE'} +\item{plot_enrichr}{Whether to plot the output using the enrichR function \link[enrichR:plotEnrich]{plotEnrich}. Defaults to 'FALSE'} \item{database_to_plot}{What database to plot the output from. Defaults to '"GO_Biological_Process_2023"'}