Merge pull request #861 from sjspielman/sjspielman/854-purge-ropenscpca

Remove rOpenScPCA from this repo
AlexsLemonade · Nov 7, 2024 · b3df18e · b3df18e
2 parents 235d5f0 + bc37e92
commit b3df18e
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Showing 26 changed files with 14 additions and 1,801 deletions.
diff --git a/.github/workflows/test_ropenscpca.yml b/.github/workflows/test_ropenscpca.yml
diff --git a/analyses/cell-type-ETP-ALL-03/renv.lock b/analyses/cell-type-ETP-ALL-03/renv.lock
@@ -2075,10 +2075,9 @@
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteUsername": "AlexsLemonade",
-      "RemoteRepo": "OpenScPCA-analysis",
-      "RemoteSubdir": "packages/rOpenScPCA",
+      "RemoteRepo": "rOpenScPCA",
       "RemoteRef": "main",
-      "RemoteSha": "d446cf35158d53e500e8bcacb08d9f2de4688b5a",
+      "RemoteSha": "fc784446f8d86b072e6f7f67287adfff598f4911",
       "Requirements": [
         "BiocParallel",
         "SingleCellExperiment",
@@ -2090,7 +2089,7 @@
         "tibble",
         "tidyr"
       ],
-      "Hash": "5c214b8e7ab3d7fd01fa32daeb51c5f8"
+      "Hash": "80a604c3be8af1ae30bcda4f96c4e290"
     },
     "rappdirs": {
       "Package": "rappdirs",

diff --git a/analyses/cell-type-nonETP-ALL-03/renv.lock b/analyses/cell-type-nonETP-ALL-03/renv.lock
@@ -2621,10 +2621,9 @@
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteUsername": "AlexsLemonade",
-      "RemoteRepo": "OpenScPCA-analysis",
-      "RemoteSubdir": "packages/rOpenScPCA",
+      "RemoteRepo": "rOpenScPCA",
       "RemoteRef": "main",
-      "RemoteSha": "a5c36235eff73530cf496c4d82715e33e79fc90e",
+      "RemoteSha": "fc784446f8d86b072e6f7f67287adfff598f4911",
       "Requirements": [
         "BiocParallel",
         "SingleCellExperiment",
@@ -2636,7 +2635,7 @@
         "tibble",
         "tidyr"
       ],
-      "Hash": "f320ea9842ac8f8eb77685aa3155751d"
+      "Hash": "80a604c3be8af1ae30bcda4f96c4e290"
     },
     "rappdirs": {
       "Package": "rappdirs",

diff --git a/analyses/hello-clusters/README.md b/analyses/hello-clusters/README.md
@@ -2,7 +2,7 @@
 
 ## Description
 
-This module provides examples of how to use clustering functionality in the `rOpenScPCA` package. 
+This module provides examples of how to use clustering functionality in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/). 
 
 When clustering scRNA-seq data, in particular when those clusters are used in downstream analyses, it is important to evaluate the quality of the clusters.
 The `rOpenScPCA` package provides several functions that leverage the [`bluster` package](https://bioconductor.org/packages/release/bioc/html/bluster.html) to facilitate performing and evaluating graph-based clustering in a reproducible manner.
@@ -11,6 +11,7 @@ The `rOpenScPCA` package provides several functions that leverage the [`bluster`
 
 The function `calculate_clusters()` can be used to perform graph-based clustering.
 By default, this function uses the Louvain algorithm with Jaccard weighting.
+
 ### Evaluate clustering
 
 `rOpenScPCA` contains several functions to calculate quality metrics for a particular clustering result:
@@ -34,14 +35,13 @@ The function `sweep_clusters()` allows you to generate clustering results from a
 
 ## Installing rOpenScPCA
 
-The `rOpenScPCA` package is disseminated in the `OpenScPCA-analysis` repository in the `packages` directory. 
+The `rOpenScPCA` package is available in the [`AlexsLemonade/rOpenScPCA` repository](https://github.com/AlexsLemonade/rOpenScPCA/).
+
 If you use this package in your analysis module, you should install and track it with `renv` as follows:
 
 ```
 # First, install rOpenScPCA
-renv::install("AlexsLemonade/OpenScPCA-analysis:packages/rOpenScPCA")
-
-
+renv::install("AlexsLemonade/rOpenScPCA")
 
 # Second, run snapshot to add the package to renv.lock
 renv::snapshot()

diff --git a/analyses/hello-clusters/renv.lock b/analyses/hello-clusters/renv.lock
@@ -1859,10 +1859,9 @@
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteUsername": "AlexsLemonade",
-      "RemoteRepo": "OpenScPCA-analysis",
-      "RemoteSubdir": "packages/rOpenScPCA",
+      "RemoteRepo": "rOpenScPCA",
       "RemoteRef": "main",
-      "RemoteSha": "c67fc87806fc8a497d18624d759342ef041e1030",
+      "RemoteSha": "fc784446f8d86b072e6f7f67287adfff598f4911",
       "Requirements": [
         "BiocParallel",
         "SingleCellExperiment",
@@ -1874,7 +1873,7 @@
         "tibble",
         "tidyr"
       ],
-      "Hash": "74da2034ae461cf45a5cf115667ff4e4"
+      "Hash": "80a604c3be8af1ae30bcda4f96c4e290"
     },
     "rappdirs": {
       "Package": "rappdirs",

diff --git a/packages/README.md b/packages/README.md
diff --git a/packages/rOpenScPCA/.Rbuildignore b/packages/rOpenScPCA/.Rbuildignore
diff --git a/packages/rOpenScPCA/DESCRIPTION b/packages/rOpenScPCA/DESCRIPTION