From 3e62aaa3e6815a62e12089c5265ddd6e59c11ecb Mon Sep 17 00:00:00 2001
From: Johannes Rainer <johannes.rainer@gmail.com>
Date: Tue, 3 Feb 2026 08:24:20 +0100
Subject: [PATCH] Add packages (issue #5)

---
 R/packages-development.txt     | 1 +
 R/packages-general.txt         | 7 +++++++
 R/packages-stats.txt           | 9 +++++++++
 R/packages-transcriptomics.txt | 1 +
 4 files changed, 18 insertions(+)

diff --git a/R/packages-development.txt b/R/packages-development.txt
index 00c6ec4..73e045f 100644
--- a/R/packages-development.txt
+++ b/R/packages-development.txt
@@ -15,3 +15,4 @@ alabaster.base
 alabaster.matrix
 alabaster.ranges
 alabaster.se
+optparse
diff --git a/R/packages-general.txt b/R/packages-general.txt
index 2e1af15..4b970a1 100644
--- a/R/packages-general.txt
+++ b/R/packages-general.txt
@@ -25,3 +25,10 @@ knitr
 AnnotationHub
 jorainer/atc
 EuracBiomedicalResearch/tidyfr
+nephro
+Category
+gridExtra
+kableExtra
+formatdown
+gtools
+extrafont
diff --git a/R/packages-stats.txt b/R/packages-stats.txt
index 4735b5f..f56f59e 100644
--- a/R/packages-stats.txt
+++ b/R/packages-stats.txt
@@ -7,3 +7,12 @@ multcomp
 survey
 limma
 caret
+ROCR
+effsize
+pcaMethods
+clusterProfiler
+survival
+treemap
+lme4
+randomForest
+venn
diff --git a/R/packages-transcriptomics.txt b/R/packages-transcriptomics.txt
index 260196a..7e470bd 100644
--- a/R/packages-transcriptomics.txt
+++ b/R/packages-transcriptomics.txt
@@ -20,3 +20,4 @@ biomaRt
 Seurat
 # cole-trapnell-lab/monocle3; disabled. needs grr, which is not available
 ensembldb
+org.Hs.eg.db