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      Introduction to Single Cell RNA-Seq Workshop

Home
Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
Single Cell Sample Preparation - Dr. Diana Burkart-Waco
Biology at True Resolution - Introduction to Single Cell and Visium Spatial Solutions
Visium Spatial Protocols - Tissue Preparation Guide
Support
Using Slack in this workshop
Using Zoom in this workshop
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (extra)
Data Reduction
Project setup
Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
scRNAseq Analysis - PART1
scRNAseq Analysis - PART2
scRNAseq Analysis - PART3
scRNAseq Analysis - PART4
scRNAseq Analysis - PART5
scRNAseq Analysis - PART6
Shiny App (extra)
Shiny App on AWS (extra)
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

Online Workshops with Slack

Text based communication will be conducted via a Slack channel. Staff will be monitoring the Slack channel to answer questions (and schedule a Zoom break out room if needed). If you know the answer to someone else’s question, feel free to answer it.

Direct Mentions

If you want to make sure that a particular person sees your comment in Slack, mention them by name, preceded by an “@” symbol.

mentioning another user

Threads

We like to use threads to keep messages on a single subject together. To reply to a comment in a thread, hold your mouse over the comment, and select the option “respond in thread.”

starting a thread

In the Slack desktop client, this opens a new window to the right of the main channel.

replying to a thread

Pinned Posts

Pinning a post can keep it from getting lost when the channel gets busy. To pin a post, hold your mouse over the post, select “more,” and choose “pin post.”

pinning a post

Pinned posts in a channel can be found quickly by clicking the channel information icon and selecting “Pinned” in the sidebar that appears.

finding pinned posts

Searching Slack

Slack history is searchable. You can specify which channels to search, which people sent a message, and message content.

searching slack