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"Intro to Bioinformatics with R" by Lisa N. Cao #189

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lfunderburk opened this Issue Aug 19, 2018 · 11 comments

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lfunderburk commented Aug 19, 2018

Description

This workshop covers an introduction to Bioinformatics with R. In this workshop, participants will have an opportunity to learn about packages such as Bioconductor https://www.bioconductor.org/ as well as SeqnR.

Requirements

The following are instructions on how to set up your environment in preparation for the Introduction to Bioinformatics with R workshop, please save some space (let's say 50mb) for datasets.

Requires: R version 3.5.0 (version can be changed if multiple versions are installed locally, but takes awhile to download so please have it ahead of time), RStudio. It is also handy to have a text editor that is good for code such as emacs or notepad++.

Environment Setup:
Bioconductor official install guide: https://www.bioconductor.org/install/

install bioconductor base and dependencies

source("https://bioconductor.org/biocLite.R")

update bioconductor base

biocLite()

Additional packages in Bioconductor (for personal interest only): https://www.bioconductor.org/packages/release/BiocViews.html#___Software

Install package SeqnR instructions http://r-forge.r-project.org/R/?group_id=220

if you are having compiling issues try

install.packages("http://download.r-forge.r-project.org/bin/windows/contrib/latest.old/seqinr_3.4-6.zip", repos=NULL)

Time and Place

Where: Room 7200, Library Research Commons, SFU Burnaby Campus

When: Tuesday, September 25, 2018 at 3:00 PM

Registration

Lesson

https://github.com/lisancao/Bioinformatics_with_R

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lisancao Sep 4, 2018

Hi Laura @lfunderburk, do you mind assigning this issue to me so I can begin adding some materials? I was going to do a more basic workshop but will probably do Intro to Bioinformatics with R instead. Thanks!

lisancao commented Sep 4, 2018

Hi Laura @lfunderburk, do you mind assigning this issue to me so I can begin adding some materials? I was going to do a more basic workshop but will probably do Intro to Bioinformatics with R instead. Thanks!

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lfunderburk Sep 6, 2018

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Hello @lisancao I tried adding you as an assignee but for some reason I am not able to add your id. Please let me know if you are able to edit directly the workshop description box.

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lfunderburk commented Sep 6, 2018

Hello @lisancao I tried adding you as an assignee but for some reason I am not able to add your id. Please let me know if you are able to edit directly the workshop description box.

gitissue

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prosoitos Sep 7, 2018

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@lfunderburk You can't assign issues to people who are not part of the SciProg team (since they are not project owners). So @lisancao should send you the information by email and you will then be able to update the issue with that information.

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prosoitos commented Sep 7, 2018

@lfunderburk You can't assign issues to people who are not part of the SciProg team (since they are not project owners). So @lisancao should send you the information by email and you will then be able to update the issue with that information.

@lfunderburk lfunderburk changed the title from Title TBA to "Intro to Bioinformatics with R" by Lisa N. Cao Sep 7, 2018

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lisancao Sep 11, 2018

Hi @lfunderburk,
For this workshop people will need to have the latest version of R (3.5.1), Rstudio (strongly preferable), and the Bioconductor package installed. (https://www.bioconductor.org/install/). Tidyverse is also highly recommended. There may also be some other packages depending on whether or not I decide try to fit in some components like importing a dataset directly from NCBI or going over some visualizations and analyses. Will post here in the next few days if I do. I will be around at 2:30pm to help anyone with setting up their environment. If there's not enough time for importing data then I will upload some datasets for people to download from my github ahead of time or at the beginning of the talk while I am doing some background on the subject.

lisancao commented Sep 11, 2018

Hi @lfunderburk,
For this workshop people will need to have the latest version of R (3.5.1), Rstudio (strongly preferable), and the Bioconductor package installed. (https://www.bioconductor.org/install/). Tidyverse is also highly recommended. There may also be some other packages depending on whether or not I decide try to fit in some components like importing a dataset directly from NCBI or going over some visualizations and analyses. Will post here in the next few days if I do. I will be around at 2:30pm to help anyone with setting up their environment. If there's not enough time for importing data then I will upload some datasets for people to download from my github ahead of time or at the beginning of the talk while I am doing some background on the subject.

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lfunderburk Sep 11, 2018

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Thank you for providing prerequisites on your workshop @lisancao

We have booked the room from 3 to 4:30. Participants usually arrive about 5 minutes before to settle in. We can also ask people to setup in advance to make the most out of the booked time. If you are concerned about people not setting up prior to the workshop, one approach would be to set the first 15 minutes to ensure everyone is on the same page.

We are currently adding descriptions and submitting to Research Commons so that the SFU community is aware of your workshop. If possible, please submit:

  1. A short description of what the workshop entails - one or two sentences summarizing your workshop is fine,
  2. Prerequisites, i.e. a laptop with R (3.5.1) and Rstudio pre-installed along with packages: Bioconductor, Tidyverse, etc.

before September 13 to add to the Research Commons description. You can add this information on the comments and I will add it in the description.

Let me know if you would like to change the title and also how I can support your workshop.

Thanks again for stepping forward! :)

Laura

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lfunderburk commented Sep 11, 2018

Thank you for providing prerequisites on your workshop @lisancao

We have booked the room from 3 to 4:30. Participants usually arrive about 5 minutes before to settle in. We can also ask people to setup in advance to make the most out of the booked time. If you are concerned about people not setting up prior to the workshop, one approach would be to set the first 15 minutes to ensure everyone is on the same page.

We are currently adding descriptions and submitting to Research Commons so that the SFU community is aware of your workshop. If possible, please submit:

  1. A short description of what the workshop entails - one or two sentences summarizing your workshop is fine,
  2. Prerequisites, i.e. a laptop with R (3.5.1) and Rstudio pre-installed along with packages: Bioconductor, Tidyverse, etc.

before September 13 to add to the Research Commons description. You can add this information on the comments and I will add it in the description.

Let me know if you would like to change the title and also how I can support your workshop.

Thanks again for stepping forward! :)

Laura

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lisancao Sep 13, 2018

Hi @lfunderburk I got the R version wrong, it's 3.5.0 since Bioconductor hasn't updated yet.

In this workshop we will go over the Bioconductor package for R, explore genomic datasets and do some preliminary analyses. Some basic R and genomic background is encouraged but not necessary to participate.

===
The following are instructions on how to set up your environment in preparation for the Introduction to Bioinformatics with R workshop, please save some space (let's say 50mb) for datasets.

Requires: R version 3.5.0 (version can be changed if multiple versions are installed locally, but takes awhile to download so please have it ahead of time), RStudio. It is also handy to have a text editor that is good for code such as emacs or notepad++.

Environment Setup:
Bioconductor official install guide: https://www.bioconductor.org/install/

##install bioconductor base and dependencies
source("https://bioconductor.org/biocLite.R")

##update bioconductor base
biocLite()

##Additional packages in Bioconductor (for personal interest only): https://www.bioconductor.org/packages/release/BiocViews.html#___Software

##Install package SeqnR instructions http://r-forge.r-project.org/R/?group_id=220
#if you are having compiling issues try
install.packages("http://download.r-forge.r-project.org/bin/windows/contrib/latest.old/seqinr_3.4-6.zip", repos=NULL)

=======================

lisancao commented Sep 13, 2018

Hi @lfunderburk I got the R version wrong, it's 3.5.0 since Bioconductor hasn't updated yet.

In this workshop we will go over the Bioconductor package for R, explore genomic datasets and do some preliminary analyses. Some basic R and genomic background is encouraged but not necessary to participate.

===
The following are instructions on how to set up your environment in preparation for the Introduction to Bioinformatics with R workshop, please save some space (let's say 50mb) for datasets.

Requires: R version 3.5.0 (version can be changed if multiple versions are installed locally, but takes awhile to download so please have it ahead of time), RStudio. It is also handy to have a text editor that is good for code such as emacs or notepad++.

Environment Setup:
Bioconductor official install guide: https://www.bioconductor.org/install/

##install bioconductor base and dependencies
source("https://bioconductor.org/biocLite.R")

##update bioconductor base
biocLite()

##Additional packages in Bioconductor (for personal interest only): https://www.bioconductor.org/packages/release/BiocViews.html#___Software

##Install package SeqnR instructions http://r-forge.r-project.org/R/?group_id=220
#if you are having compiling issues try
install.packages("http://download.r-forge.r-project.org/bin/windows/contrib/latest.old/seqinr_3.4-6.zip", repos=NULL)

=======================

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lfunderburk Sep 24, 2018

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Hello @lisancao

Let me know how I can support you in tomorrow's workshop.

I have class at 2:30 but I can meet you earlier during the afternoon to setup, get to the place, etc.

Laura

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lfunderburk commented Sep 24, 2018

Hello @lisancao

Let me know how I can support you in tomorrow's workshop.

I have class at 2:30 but I can meet you earlier during the afternoon to setup, get to the place, etc.

Laura

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lisancao Sep 24, 2018

lisancao commented Sep 24, 2018

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lfunderburk Sep 24, 2018

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Hello Lisa,

I can meet you at the library entrance. Unfortunately my class runs from 2:30 - 3:30 so I would not be able to meet you after my class is over, but I can meet you before.

What is your email address? I can forward it to Research Commons so they can get in touch with you. They have provided sticky notes in the past and can help with the room.

Laura

Member

lfunderburk commented Sep 24, 2018

Hello Lisa,

I can meet you at the library entrance. Unfortunately my class runs from 2:30 - 3:30 so I would not be able to meet you after my class is over, but I can meet you before.

What is your email address? I can forward it to Research Commons so they can get in touch with you. They have provided sticky notes in the past and can help with the room.

Laura

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lisancao commented Sep 24, 2018

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lisancao Sep 25, 2018

All workshop materials are available here:
https://github.com/lisancao/Bioinformatics_with_R

lisancao commented Sep 25, 2018

All workshop materials are available here:
https://github.com/lisancao/Bioinformatics_with_R

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