update vignettes for 2.0.3

ncborcherding · May 4, 2024 · 7cf56eb · 7cf56eb
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diff --git a/vignettes/articles/Loading.Rmd b/vignettes/articles/Loading.Rmd
@@ -63,11 +63,12 @@ contig_list <- list(S1, S2, S3, S4)
 Beyond the default 10x Genomic Cell Ranger pipeline outputs, scRepertoire supports the following **single-cell** formats: 
 
 * AIRR  
-* BD Rhapsody Multiomic Immune Profiling  
+* [BD Rhapsody](https://www.bd-rhapsody.com/) Multiomic Immune Profiling  
 * [Immcantation](https://immcantation.readthedocs.io/en/stable/index.html)  
 * JSON-formatted contig data  
 * [MiXCR](https://pubmed.ncbi.nlm.nih.gov/25924071/)  
-* [Omniscope](https://www.omniscope.ai/)  
+* [Omniscope](https://www.omniscope.ai/) OS-T/OS-B
+* [Parse](https://www.parsebiosciences.com/) Evercode TCR/BCR
 * [TRUST4](https://pubmed.ncbi.nlm.nih.gov/33986545/)  
 * [WAT3R](https://pubmed.ncbi.nlm.nih.gov/35674381/)  
 

diff --git a/vignettes/articles/Running_Escape.Rmd b/vignettes/articles/Running_Escape.Rmd
@@ -218,6 +218,7 @@ ggplot(data = as.data.frame(enrichment.scores),
   theme_classic() + 
   theme()
 ```
+
 Multi-core support is for all methods is available through [BiocParallel](https://bioconductor.org/packages/release/bioc/html/BiocParallel.html). To add more cores, use the argument **BPPARAM** to ```escape.matrix()```. Here we will use the ```SnowParam()``` for it's support across platforms and explicitly call 2 workers (or cores).
 
 ```{r tidy=FALSE, eval=FALSE}