Merge pull request #2 from iibadshah/main

protools2 v0.2.9

Author: iibadshah

.Rbuildignore

@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$

DESCRIPTION

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 Package: protools2
 Type: Package
-Title: A set of tools for proteomics and phosphoproteomics data analysis
-Version: 0.2.1
-Date: 2023-01-07
-Author: Pedro Rodriguez Cutillas
+Title: A Set Of Tools For Proteomics And Phosphoproteomics Data Analysis
+Version: 0.2.9
+Date: 2023-06-22
+Author: Pedro Rodriguez Cutillas, Irbaz I. Badshah
 Maintainer: Pedro Rodriguez Cutillas <p.cutillas@qmul.ac.uk>
 Description: Reads and normalizes data from Pescal. Does statistical analysis using limma or t-test. It also incoroporates functions for KSEA, pathway analysis and network visualization tools.
-License: CC-BY-NC-ND 4.0 
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends: 
-    R (>= 2.10)
-Imports: 
-    doParallel,
-    dplyr,
-    foreach,
-    ggplot2,
+    R (>= 3.5.0)
+Imports:
+    knitr,
+    devtools,
+    webshot,
+    webshot2,
+    flextable,
+    kableExtra,
     ggpubr,
+    gplots,
+    grid,
+    gridExtra,
+    cowplot,
     ggrepel,
-    igraph,
-    limma,
+    reshape2,
+    viridisLite,
+    plotly,
+    heatmaply,
+    umap,
+    openxlsx,
     readxl,
-    stringr
+    tools,
+    igraph,
+    data.table,
+    magrittr,
+    tibble,
+    ggplot2,
+    dplyr,
+    tidyr,
+    readr,
+    purrr,
+    stringr,
+    forcats,
+    dtplyr,
+    parallel,
+    foreach,
+    doParallel,
+    limma
 RoxygenNote: 7.2.3

LICENSE

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+YEAR: 2023
+COPYRIGHT HOLDER: protools2 authors

LICENSE.md

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+# MIT License
+
+Copyright (c) 2023 protools2 authors
+
+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.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
 exportPattern("^[[:alpha:]]+")
+export(complex_heatmap)
+export(fix_combiPeptData)
+export(installer)
+export(mergeDTs)
+export(myHeatMap_With_PValues)
+export(remove_outlier_samples_from_dataset_edit)
+export(umap_and_plot)
+export(update_protools)