Workshop on the
3D RNASeq Analysis Tool
Researchers at the James Hutton Institute and the University of Dundee-Plant Sciences have developed the 3D RNA-Seq Analysis Tool for the comprehensive differential expression, alternative splicing analysis and visualisation of RNASeq Data.
https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/
It runs the analysis through a user-friendly graphical interface, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures and customerised analysis reports.
The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to take control of the analysis of their RNA-seq data.
https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/
It runs the analysis through a user-friendly graphical interface, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures and customerised analysis reports.
The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to take control of the analysis of their RNA-seq data.
In order to provide training in this new software tool GARNet are hosting a workshop at the University of Leeds that is led by the creators of the 3D App, Wenbin Guo and Runxuan Zhang.
This workshop will take places at the University of Leeds and is hosted by GARNet Committee Member Yoselin Benitez-Alfonso.
Workshop Date: Thursday October 24th 12pm until Friday October 25th 5pm.
Location: Leeds Institute for Data Analytics, University of Leeds, Leeds, LS2 9JT
Workshop Cost: £30
Number of Delegates: 20
How to Apply:
1. Please write a short message (<200 words) to GARNet coordinator Geraint Parry (geraint@garnetcommunity.org.uk) explaining why you would like to attend this workshop. Deadline for this application is Monday September 23rd 12pm.
2. The organising team will then decide who will attend the workshop. Preference will be given to people who will be able to teach others at their host institution about use of the 3D RNAseq tool as well as to those who will be imminently analysing their own RNA-Seq data. We will inform successful applicants by October 1st so that you can arrange your travel to and accommodation in Leeds.
3. If you have more detailed questions about visualising your data with the 3D App, Wenbin and Runxuan will be available to offer 1-2-1 advice during 30minute sessions on the second afternoon of the workshop.
If you would like to take advantage of this opportunity then please indicate this in your application. There are only six of these sessions available so applying for these is not a pre-requisite for selection to attend the remainder of the meeting.
4. After the meeting we will publish all meeting presentations on the GARNet website.
Workshop Schedule
Thursday October 24th 2019
12pm: Arrival and Lunch
1.15pm: Yoselin Benitez-Alfonso- Welcome to the University of Leeds
1.30pm: Runxuan Zhang- A suite of computational solutions for improved gene and transcript level analysis using RNA-seq.
2.30pm: Presenter fropm Earlham Institute- Data management hands-on session: Taking care of your data.
4.00pm: Tea Break
4.30pm: Pingtao Ding, The Sainsbury Laboratory, Norwich- Proof of Concept: Using the 3D RNA-Seq app to analyse expression changes under different immune activation conditions.
5.30pm: Runxuan Zhang and Wenbin Guo- Preparation for the hands on session: downloading the data, etc
7pm: Evening meal and drinks in Leeds
Friday October 25th 2019
9.00am: Runxuan Zhang and Wenbin Guo- Hands on session with 3D RNA-Seq App
10.30am: Tea Break
11.00am: Hands on session with 3D RNA-Seq App, continued
11.45am: Recapping main features of 3D RNA-Seq App and General Q+A
1.00pm: Lunch and General Meeting end
2.00pm: 1-2-1 sessions on analysis of own data. To be arranged in advance (see above).
Workshop details
Accommodation
Ther University of Leeds has kindly provided a list of local hotels with prices and contacts.
Please download the list here.
Catering
We will of course cater for vegetarians but please let Geraint Parry know if you have any other dietary requirements.
If you have any questions about the workshop please contact Geraint Parry.
GARNet is a UKRI-BBSRC supported network that supports fundamental plant science researchers in the UK and beyond!
Ther University of Leeds has kindly provided a list of local hotels with prices and contacts.
Please download the list here.
Catering
We will of course cater for vegetarians but please let Geraint Parry know if you have any other dietary requirements.
If you have any questions about the workshop please contact Geraint Parry.
GARNet is a UKRI-BBSRC supported network that supports fundamental plant science researchers in the UK and beyond!
