Merge branch 'master' into develop

trn13 · Jul 15, 2021 · 7c9a047 · 7c9a047
2 parents 62a43ef + ee2cba1
commit 7c9a047
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 2 deletions.
diff --git a/vignettes/hashing_vignette.Rmd b/vignettes/hashing_vignette.Rmd
@@ -117,7 +117,7 @@ pbmc.hashtag <- NormalizeData(pbmc.hashtag, assay = 'HTO', normalization.method
 
 Here we use the Seurat function `HTODemux()` to assign single cells back to their sample origins.
 
-```{r hashtag_demux}
+```{r hashtag_demux, results = FALSE}
 # If you have a very large dataset we suggest using k_function = "clara". This is a k-medoid clustering function for large applications
 # You can also play with additional parameters (see documentation for HTODemux()) to adjust the threshold for classification
 # Here we are using the default settings
@@ -238,7 +238,7 @@ hto12 <- NormalizeData(hto12, assay = "HTO", normalization.method = "CLR")
 
 ## Demultiplex data
 
-```{r demux}
+```{r demux, results = FALSE}
 hto12 <- HTODemux(hto12, assay = "HTO", positive.quantile = 0.99)
 ```
 

diff --git a/vignettes/vignettes.yaml b/vignettes/vignettes.yaml
@@ -216,3 +216,17 @@
       reference: https://doi.org/10.1186/s12859-020-3538-2
       citation: Ekiz et. al., BMC Bioinformatics 2020
       source: https://github.com/atakanekiz/CIPR-Package
+
+    - name: miQC
+      title: Running miQC on Seurat objects
+      link: http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/miQC.html
+      reference: https://www.biorxiv.org/content/10.1101/2021.03.03.433798v1
+      citation: Hippen et. al., bioRxiv 2021
+      source: https://github.com/greenelab/miQC
+
+    - name: tricycle
+      title: Running estimate_cycle_position from tricycle on Seurat Objects
+      link: http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/tricycle.html
+      reference: https://doi.org/10.1101/2021.04.06.438463
+      citation: Zheng et. al., bioRxiv 2021
+      source: https://www.bioconductor.org/packages/release/bioc/html/tricycle.html