add index page

README.md

@@ -23,5 +23,7 @@ Starting with the expression counts matrix, this workshop will cover the followi
 1. Marker gene/cell annotation
 
 
+Webpages:
 
+https://biocellgen-private.svi.edu.au/amsi_day1-hands-on-scrnaseq-analysis-workshop-2020-11-30_svi/public/index.html
 

analysis/index.Rmd

+---
+title: "BioInfoSummer Single-cell RNA-seq analysis workshop"
+site: workflowr::wflow_site
+output:
+  workflowr::wflow_html:
+    toc: true
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+##  Introduction   
+
+In this workshop, we will introduce the data infrastructure for scRNAseq analysis 
+in R and practice a workflow of scRNAseq analysis; from pre-processing, quality
+control to dimensionality reduction aand clustering. We will then demonstrate the
+usage of marker genes for cell type annotation and an automatic approach for matching
+query cells to a reference altas with labels. 
+
+
+1. [single-cell RNAseq analysis workflow for cell type identification](BIOS_analysis-workflow.html)