v1.1.5

.github/workflows/sync-to-org.yml

@@ -0,0 +1,67 @@
+name: "Sync main & tags to org (SSH, prune)"
+
+on:
+  push:
+    branches:
+      - main       # only when main changes
+    tags:
+      - "*"        # and on any tag push
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  sync:
+    # only from the source repo (so the fork doesn't need secrets)
+    if: github.repository == 'yqkiuo/BreastSubtypeR'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Ensure secret exists
+        run: |
+          if [ -z "${{ secrets.MIRROR_DEPLOY_KEY }}" ]; then
+            echo "::error:: Secret MIRROR_DEPLOY_KEY is missing in yqkiuo/BreastSubtypeR."
+            exit 1
+          fi
+
+      - name: Start ssh-agent & add deploy key
+        uses: webfactory/ssh-agent@v0.9.0
+        with:
+          ssh-private-key: ${{ secrets.MIRROR_DEPLOY_KEY }}
+
+      - name: Trust github.com host key
+        run: |
+          mkdir -p ~/.ssh
+          ssh-keyscan -t rsa,ecdsa,ed25519 github.com >> ~/.ssh/known_hosts
+
+      - name: Configure git identity
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+
+      - name: Add mirror remote (org fork)
+        run: |
+          git remote add mirror git@github.com:JohanHartmanGroupBioteam/BreastSubtypeR.git
+          git remote -v
+
+      - name: Fetch origin & mirror (for safe lease)
+        run: |
+          set -e
+          git fetch --tags --prune origin
+          git fetch --prune origin +refs/heads/*:refs/remotes/origin/*
+          git fetch --tags --prune mirror
+          git fetch --prune mirror +refs/heads/*:refs/remotes/mirror/*
+
+      - name: Push main & tags to mirror (prune deleted tags)
+        run: |
+          set -e
+          # Push main with a safe force (only if mirror hasn't moved unexpectedly)
+          git push --force-with-lease mirror refs/remotes/origin/main:refs/heads/main
+          # Push all tags, pruning tag deletions
+          git push --prune --tags mirror

DESCRIPTION

@@ -10,8 +10,8 @@ Description: BreastSubtypeR provides an assumption-aware, multi-method framework
     (iBreastSubtypeR) is included for interactive analyses and to support users
     without programming experience.
 Encoding: UTF-8
-Version: 1.1.4
-biocViews: RNASeq, Software, GeneExpression, Classification
+Version: 1.1.5
+biocViews: RNASeq, Software, GeneExpression, Classification, Preprocessing, Visualization
 Authors@R: c(
     person(given = "Qiao", family = "Yang", 
 	   role = c("aut", "cre"), 
@@ -59,4 +59,4 @@ License: GPL-3
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "collate"))
 LazyData: FALSE
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NAMESPACE

@@ -15,13 +15,10 @@ export(Vis_boxplot)
 export(Vis_heatmap)
 export(Vis_pie)
 export(iBreastSubtypeR)
-export(runShinyBreastSubtypeR)
 import(Biobase)
 import(ComplexHeatmap)
 import(RColorBrewer)
 import(circlize)
-import(e1071)
-import(ggplot2)
 import(ggrepel)
 import(grid)
 import(impute)
@@ -35,7 +32,30 @@ importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(data.table,data.table)
 importFrom(data.table,set)
+importFrom(dplyr,across)
+importFrom(dplyr,everything)
+importFrom(dplyr,mutate)
 importFrom(dplyr,select)
+importFrom(e1071,naiveBayes)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,coord_polar)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_boxplot)
+importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_text)
+importFrom(ggplot2,geom_vline)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_color_manual)
+importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_classic)
+importFrom(ggplot2,theme_minimal)
+importFrom(ggplot2,theme_void)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,pdf)
 importFrom(graphics,barplot)
@@ -48,6 +68,7 @@ importFrom(stats,cor)
 importFrom(stats,cor.test)
 importFrom(stats,dist)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,prcomp)
 importFrom(stats,quantile)
 importFrom(tidyselect,everything)

NEWS.md

@@ -1,9 +1,9 @@
-# BreastSubtypeR 1.1.3
+# BreastSubtypeR 1.1.5
 
 ## Highlights
 - Paper published in *NAR Genomics and Bioinformatics* (2025), **Editor’s Choice** (DOI: 10.1093/nargab/lqaf131).
-- **New:** Support for raw RNA-seq counts (requires gene lengths).
-- Major **iBreastSubtypeR** refresh: cleaner UX, smarter AUTO guidance, consistent exports.
+- Support for raw RNA-seq counts (requires gene lengths).
+- **iBreastSubtypeR** refresh: cleaner UX, smarter AUTO guidance, consistent exports.
 - Refined, data-driven thresholds for ER/HER2 skew detection in AUTO.
 - Broader input-validation across the subtyping pipeline.
 
@@ -41,4 +41,4 @@
 ## Upgrade Notes
 - Raw RNA-seq counts are supported **from v1.1.3 onward** (requires gene lengths).
 - If you previously parsed `BS` / `BS.Subtype`, switch to **`Call_5class` / `Call_4class`**.
-- Package API unchanged (the `Subtype` argument remains).
+- Package API unchanged.