Bioc review

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: immGLIPH
 Title: Grouping of Lymphocyte Interactions by Paratope Hotspots
-Version: 0.99.2
+Version: 0.99.3
 Authors@R: c(
     person("Nick", "Borcherding", role = c("aut", "cre"),
            email = "ncborch@gmail.com")
@@ -26,8 +26,7 @@ Depends:
 Imports:
     stringdist,
     igraph,
-    foreach,
-    doParallel,
+    BiocParallel,
     parallel,
     stringr,
     stats,

NAMESPACE

@@ -8,6 +8,5 @@ export(getRandomSubsample)
 export(loadGLIPH)
 export(plotNetwork)
 export(runGLIPH)
-import(foreach)
 import(grDevices)
 import(viridis)

NEWS.md

@@ -1,3 +1,36 @@
+# immGLIPH 0.99.4
+
+* Added a Validation section to the README with concordance metrics
+  against the published GLIPH and GLIPH2 cluster vectors from
+  Glanville et al. (2017) and Huang et al. (2020). With paper-matched
+  parameters, immGLIPH reproduces the published cluster vectors at
+  ARI 0.985 (Glanville) and 0.863 (Huang) on the intersection of
+  shared CDR3s. Full benchmark code lives at
+  [BorchLab/immGLIPH-benchmark](https://github.com/BorchLab/immGLIPH-benchmark).
+* Fixed `clusterScoring()` failure in the clonal-expansion-enrichment
+  test when a cluster contains more members than the reference pool
+  has rows. The null draw now uses `replace = TRUE` (bootstrap),
+  matching the V-gene null and the statistically appropriate choice
+  for resampling. Surfaced on the Huang 2020 benchmark.
+
+# immGLIPH 0.99.3
+
+* Replaced `foreach`/`doParallel` with `BiocParallel` for parallelization
+  across all functions per Bioconductor recommendations.
+* Replaced `devtools::install_github()` references with
+  `BiocManager::install()` in vignette and error messages.
+* Updated vignette to use `SingleCellExperiment` instead of `Seurat` for
+  the single-cell workflow example.
+* Fixed `combineTCR()` example in vignette (removed obsolete `cells`
+  argument).
+* Made more vignette code chunks evaluable (`clusterScoring()`,
+  `deNovoTCRs()`, `plotNetwork()` examples).
+* Noted that `scRepertoire` and `immApex` are Bioconductor packages.
+* Replaced iterative for-loop list growing with vectorized alternatives
+  (`lapply()`, `vapply()`, `Reduce()`).
+* Standardized code spacing around operators and after commas per
+  Bioconductor coding style.
+
 # immGLIPH 0.99.2
 
 * Fixing roxygen documentation issue creating warnings.