JMP Genomics - Academic Learning Series 2021 Part 3

[#1]

Other videos in this series:

• Part 1: Introduction to JMP® Genomics and Importing Data into JMP Genomics

• Part 2: Expression Data Analysis

• Part 4 GWS, Genotype Analysis and Genetics 

[Patel213]

Hello 

This is Priyanka, working at university of Illinois as a post doc, we talked about JMP genomics 

Pl find herewith attached screenshot for JMP genomics license  recent version we recently bought for analyzing single cell genomics data 

now the weird thing I found is we don't have any option to import single cell data in analytical process dialog box below the Import VCF files button (pl find herewith attached screenshot 1 )

the option which I saw in one of webinar(https://community.jmp.com/t5/Melisa-Muhamed-s-Blog/JMP-Genomics-Academic-Learning-Series-2021-Part-3...) I am going through to analyze single cell data (Pl find herweith attached screenshot2 ), do we have to install some plugin to make that option available

Request to please resolve the query 

Thanks 

Screenshot 1  

    

Screenshot 2 from webinar 

[gail_massari]

Hi  Priyanka @Patel213 .  If you includee @mention (in this case, @Chris_Kirchberg) in your comments, they will go directly to the person who could help.   If Chris can't help he will find someone who can.

[Chris_Kirchberg]

Hi @Patel213 ,

What you are looking for is in the newest version of JMP Genomics, JMP Genomics 10. If you go to the Help menu item at the top left and then choose About JMP. There will be the version number as well as the SITE ID number.

It is likely you have an older version and need to obtain the newest version. @pany_allen, your academic sales person,  should be able to help you and your institution get access to the latest version.

Best,

[Chris_Kirchberg]

@Patel213 , I forgot to mention that if you want to use t-SNE and UMAP, you would also need to install R on the same computer. Here is a link to help documentation that gives some guidance regarding these two packages and JMP Genomics.  Here is another link to the documentation for the Basic Single-Cell RNA-Seq Workflow.

Here is some additional details about adding those packages and what you have to do to enable them for JMP Genomics:

Instructions for R Installation:

1. If R is not installed on your machine, please go to https://www.r-project.org/ to download the latest version of R.
2. If R is already installed, make sure only one version of R is available. If any problems happen when calling R, try to uninstall and update to the latest version.
3. Install Rtsne and UMAP packages by type install.packages("Rtsne") and install.packages("UMAP") in R console.
4. Type library("Rtsne") and library("UMAP") in R console to make sure not errors occurred
5. For more information regarding these two packages, check out their manual pages:
   • Rtsne: https://cran.r-project.org/web/packages/Rtsne/index.html
   • UMAP: https://cran.r-project.org/web/packages/umap/index.html

Modify the sasv9.cfg File to Include the -RLANG Option in the SAS System File:

You must set this option or you will encounter error messages when attempting to use this Add-In.

1. Navigate to the location of the sasv9.cfg file on your computer. Typically, this file is located in the C:\Program Files\SASHome\SASFoundation\9.4\nls\en\ directory;
2. Open the file with a text editor;
3.  Type -RLANG in the first line of the file;
4. Save and close the sasv9.cfg file.

Refer to the RLANG System Option page (http://support.sas.com/documentation/cdl/en/imlug/63541/HTML/default/viewer.htm#imlug_r_sect003.htm) for more information.