kaozkai · Mar 6, 2026 · Mar 9, 2026 · Apr 2, 2026
diff --git a/README.md b/README.md
@@ -1,3 +1,4 @@
+![clustirr logo](inst/extdata/logo.png)
 # ClustIRR: Clustering of Immune Receptor Repertoires
 
 ![Build Status](https://github.com/snaketron/ClustIRR/actions/workflows/r.yml/badge.svg)
@@ -37,5 +38,5 @@ Case studies are provided in the directory /vignettes
 
 ## Workflow & output 
 
-![clustirr workflow](/inst/extdata/logo.png)
+![clustirr workflow](/inst/extdata/workflow.png)
 
diff --git a/inst/extdata/logo.png b/inst/extdata/logo.png
diff --git a/inst/extdata/workflow.png b/inst/extdata/workflow.png
diff --git a/inst/extdata/logo.svg → inst/extdata/workflow.svg b/inst/extdata/logo.svg → inst/extdata/workflow.svg
diff --git a/vignettes/User_manual_introduction.Rmd b/vignettes/User_manual_introduction.Rmd
@@ -26,6 +26,10 @@ library(patchwork)
 options(digits=2)
 ```
 
+```{r graphic_logo, echo = FALSE, fig.align="left", out.width='100%'}
+knitr::include_graphics("../inst/extdata/logo.png")
+```
+
 # Introduction
 
 Adaptive immunity employs diverse immune receptor repertoires (IRRs; B-
@@ -79,7 +83,7 @@ BiocManager::install("ClustIRR")
 # ClustIRR algorithm
 
 ```{r graphic, echo = FALSE, fig.align="left", out.width='100%'}
-knitr::include_graphics("../inst/extdata/logo.png")
+knitr::include_graphics("../inst/extdata/workflow.png")
 ```
 
 ## Input