[Blocked till bioc 3.21] Add scRepertoire as dependency and remove quietTCR sourcecode

DESCRIPTION

@@ -13,8 +13,10 @@ LazyDataCompression: xz
 RoxygenNote: 7.3.2
 biocViews: Software, ImmunoOncology, SingleCell, Classification, Annotation, Sequencing
 Depends: 
-	R (>= 4.0)
-Imports: stringr, 
+	R (>= 4.0),
+	scRepertoire
+Imports:
+	stringr, 
 	SeuratObject,
 	SingleCellExperiment,
 	rlang,
@@ -24,7 +26,7 @@ Imports: stringr,
 	Matrix, 
 	matrixStats,
 	SummarizedExperiment,
-        stats,
+    stats,
 	stringdist, 
 	utils
 Suggests: 
@@ -38,8 +40,8 @@ Suggests:
 	patchwork,
 	ggplot2,
 	spelling,
-        testthat (>= 3.0.0)
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Language: en-US
-URL: https://github.com/ncborcherding/Trex/
-BugReports: https://github.com/ncborcherding/Trex/issues
+URL: https://github.com/BorchLab/Trex/
+BugReports: https://github.com/BorchLab/Trex/issues

NAMESPACE

@@ -3,15 +3,12 @@
 export(CoNGAfy)
 export(annotateDB)
 export(maTrex)
-export(quietTCRgenes)
 export(runTrex)
 importFrom(Matrix,colSums)
 importFrom(Matrix,sparse.model.matrix)
 importFrom(SeuratObject,CreateAssayObject)
 importFrom(SeuratObject,CreateDimReducObject)
 importFrom(SeuratObject,CreateSeuratObject)
-importFrom(SeuratObject,DefaultAssay)
-importFrom(SeuratObject,VariableFeatures)
 importFrom(SingleCellExperiment,"reducedDim<-")
 importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SingleCellExperiment,colData)
@@ -28,4 +25,3 @@ importFrom(stringdist,stringdist)
 importFrom(stringr,str_sort)
 importFrom(stringr,str_split)
 importFrom(tensorflow,tf)
-importFrom(utils,getFromNamespace)

NEWS

@@ -4,7 +4,8 @@ CHANGES IN VERSION 0.99.12
 * Incorporating immApex Usage
 * Update ```CoNGAfy()``` to support all versions of Seurat
 * Update trex_example to Seurat v5
-* Updated ```quietTCRgenes()``` to used VariableFeatures() call
+* Add `scRepertoire` as a dependency
+* Updated ```quietTCRgenes()``` to used VariableFeatures() call, and moved definition to `scRepertoire`
 
 
 CHANGES IN VERSION 0.99.11

vignettes/vignette.Rmd

@@ -37,7 +37,7 @@ suppressMessages(library(patchwork))
 
 To show the multiple options of Trex, the example data is derived from [GSE167118](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167118) - a cohort of CITE-seq data derived from severe COVID-19 patients. The [corresponding manuscript](https://pubmed.ncbi.nlm.nih.gov/33622974/) is excellent. The data example built into the package (trex_example) is derived from randomly sampling the single-cells from patient 17. 
 
-This is a standard workflow based on the [WNN](https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html) Seurat process. However, Trex will work for Bioconductor/Single-Cell Experiment workflows as well. The major exception is the addition of ```quietTCRgenes()```, which removed T cell receptor genes from the variable gene list used for ```runPCA()```. In addition, the final 2 rows of the ADT assay are removed, as they are antibodies for specific TCRs. This prevents the weighting of the embedding based on both genes and clonotype information. Removing T cell receptor genes is also a common practice before dimensional reduction. 
+This is a standard workflow based on the [WNN](https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html) Seurat process. However, Trex will work for Bioconductor/Single-Cell Experiment workflows as well. The major exception is the addition of ```scRepertoire::quietTCRgenes()```, which removed T cell receptor genes from the variable gene list used for ```runPCA()```. In addition, the final 2 rows of the ADT assay are removed, as they are antibodies for specific TCRs. This prevents the weighting of the embedding based on both genes and clonotype information. Removing T cell receptor genes is also a common practice before dimensional reduction. 
 
 
 ```{r, eval=FALSE}