-
Notifications
You must be signed in to change notification settings - Fork 10
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Update rna_seq_2.md Made some small changes, adjusted wording to be more clear. * Update rna_seq_3.md * Update rna_seq_4.md * Update rna_seq_5.md * Update rna_seq_6.md * Update rna_seq_7.md * Update rna_seq_8.md * Update rna_seq_1.md * minor text edits for conda lesson * Update rna_seq_2.md * Update rna_seq_3.md * Update rna_seq_3.md * Update rna_seq_4.md * Update rna_seq_4.md * Adding workshop resources (#469) * adding conda workshop screenshots for attendees * communication image * resize communication image * adding launch binder and export binder file imgs * aws screen img Co-authored-by: marisalim <[email protected]> Co-authored-by: Marisa Lim <[email protected]> * RNAseq on Cavatica lesson fixes (#464) * fixed image links across all lessons * Added network access admonition box * fixed error in number of files in cavatica-view lesson * updated to RNA-Seq naming convention * updated home page RNA-Seq carousal * updated home pg carousal with conda lesson blurb * added trainling mailing list to the workshops box on home pg * added training mailing list to announce bar * added july workshops to box on home pg * updated lfc shrink text * added mailing list icon in footer * fixed broken links to kf rnaseq workflow * correction to GTF reference file selection * updated R scripts with GTF file * updated deseq2 app lesson with new analysis setup vidlet and steps * updated the vidlet to tag and download DESeq2 outputs * fixed broken link * correction to conda description in home pg * corrections to data cruncher scripts * updated KF lesson with RNA-Seq syntax * updated intro to R workshop link on home pg * updated lfc shrinkage text * fixed right render issue on chrome * updated workshop box with august wrkshps * Lesson edits and minor fixes before merge to stable (#471) * text corrections based on jeremy's suggestion * standardize to RNA-Seq on landing pgs * a->an and an oxford comma just because Co-authored-by: marisalim <[email protected]> Co-authored-by: Jeremy Walter <[email protected]> * clarify vidlet topics, add export option per suggestions from Dirk's JOSE review * add note about binder (base) * updated reviewer list for PRs (#479) * Updates to AWS tutorial (#478) * Updates to AWS tutorial with new screenshots and correction to AMI choice * Fixed links and corrections to build statements * Fixed links to open in new tab * add sept oct nov workshops (#474) * add sept and oct workshops * add november workshops * fix conda workshop link * hyperlink calendar text not past workshop text * add sep oct nov workshops * consistent titles * added august workshops and minor edits * updated links and minor text fixes * update comment pr workflow Co-authored-by: Saranya Canchi <[email protected]> * Update README.md (#480) * Update README.md * updated with august and july workshops * added training mailing list * fixed email link * minor text edit * updated email alias Co-authored-by: Saranya Canchi <[email protected]> * added release notes for december (#482) Co-authored-by: HigginsD3b <[email protected]> Co-authored-by: marisalim <[email protected]> Co-authored-by: Marisa Lim <[email protected]> Co-authored-by: Jeremy Walter <[email protected]> Co-authored-by: Rayna M Harris <[email protected]>
- Loading branch information
6 people
authored
Dec 10, 2021
1 parent
6642b2b
commit 99d26dc
Showing
33 changed files
with
238 additions
and
96 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| # CFDE Training Resources | ||
|
|
||
| This repository builds the public training materials for the CFDE: https://training.nih-cfde.org | ||
| The `stable` branch of this repository builds the public training materials for the CFDE at https://training.nih-cfde.org. The `dev` branch contains updates that will be merged as part of the next [release](https://github.com/nih-cfde/training-and-engagement/blob/dev/docs/TrainingRepoReleasePlan/TrainingRepo-Release-Plan.md). | ||
|
|
||
| The training website hosts tutorials and resources to learn how to perform bioinformatic analyses and access data. The GitHub repository contains CFDE internal resources, including the [website style guide](./docs/Website-Style-Guide/0index.md) and [website release protocol](./docs/TrainingRepoReleasePlan/TrainingRepo-Release-Plan.md). | ||
|
|
||
|
|
@@ -13,12 +13,74 @@ We welcome suggestions for improvements as well as tutorial topics. Submit all t | |
| ## Workshops | ||
|
|
||
| <div> | ||
| <p><div style="font-size:22px; font-style: italic">Check out our events calendar for <a href="https://www.nih-cfde.org/events/" target="_blank" rel="noopener" style="color:#336699;">upcoming workshops !</a></div></p> | ||
| <p><div style="font-size:24px; font-style: italic"><i>Check out our <a href="https://www.nih-cfde.org/events/" target="_blank" rel="noopener" style="color:#336699;">events calendar</a> for upcoming workshops!</i></div></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:22px; font-style: italic">Past workshops:</a></div></p> | ||
| <p><div style="font-size:24px; font-style: italic">Join our <a href="mailto:CFDE-Training%20<[email protected]" target="_blank" rel="noopener" style="color:#336699;">training mailing list</a> for all the latest updates.</div></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:24px; font-style: italic">Past workshops:</a></div></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/An-Introduction-to-UNIX:-November-17,-2021" target="_blank" rel="noopener" style="color:#336699;">Introduction to UNIX Command Line</a></div><i>Novemver 17, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/A-Hands-On-Introduction-to-AWS:-November-10,-2021" target="_blank" rel="noopener" style="color:#336699;">Introduction to Amazon Web Services/Elastic Cloud Computing</a></div><i>November 10, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/Introduction-to-R:-October-13,-2021" target="_blank" rel="noopener" style="color:#336699;">Introduction to R</a></div><i>October 13, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/A-Hands-On-Introduction-to-Conda:-October-6,-2021" target="_blank" rel="noopener" style="color:#336699;">A Hands On Introduction to Conda</a></div><i>October 6, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/RNA-Seq-in-the-cloud:-June-21-&-23,-2021" target="_blank" rel="noopener" style="color:#336699;">RNA-Seq in the Cloud</a></div><i>September 21 & 23, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://osf.io/txcw8/" target="_blank" rel="noopener" style="color:#336699;">RNA-Seq Concepts, Design and Workflows</a></div><i>September 22, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/making-use-of-on-demand-cloud-computers-from-amazon-web-services.html" target="_blank" rel="noopener" style="color:#336699;">Cloud Computing with AWS</a></div><i>August 31, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/executing-large-analyses-on-hpc-clusters-with-slurm.html" target="_blank" rel="noopener" style="color:#336699;">Using SLURM on HPC</a></div><i>August 26, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/automating-your-analyses-with-the-snakemake-workflow-system.html" target="_blank" rel="noopener" style="color:#336699;">Automating using Snakemake</a></div><i>August 25, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/keeping-track-of-your-files-with-version-control.html" target="_blank" rel="noopener" style="color:#336699;">Using Version Control</a></div><i>August 24, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/automating-your-analyses-and-executing-long-running-analyses-on-remote-computers.html" target="_blank" rel="noopener" style="color:#336699;">Automating Analyses</a></div><i>August 19, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/structuring-your-projects-for-current-and-future-you.html" target="_blank" rel="noopener" style="color:#336699;">Structuring Project Folders</a></div><i>August 17, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/installing-software-on-remote-computers-with-conda.html" target="_blank" rel="noopener" style="color:#336699;">Installing Software with Conda</a></div><i>August 13, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/running-programs-on-remote-computers-and-retrieving-the-results.html" target="_blank" rel="noopener" style="color:#336699;">Running Programs and Retrieving Results</a></div><i>August 12, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/connecting-to-remote-computers-with-ssh.html" target="_blank" rel="noopener" style="color:#336699;">Connecting Remote Computers with SSH</a></div><i>August 10, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/creating-and-modifying-text-files-on-remote-computers.html" target="_blank" rel="noopener" style="color:#336699;">Creating & Modifying Text Files</a></div><i>August 4, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://ngs-docs.github.io/2021-august-remote-computing/introduction-to-the-unix-command-line.html" target="_blank" rel="noopener" style="color:#336699;">Introduction to UNIX Command Line</a></div><i>August 3, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/Introduction-to-R:-July-28,-2021" target="_blank" rel="noopener" style="color:#336699;">Introduction to R</a></div><i>July 28, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://osf.io/txcw8/" target="_blank" rel="noopener" style="color:#336699;">RNA-Seq Concepts, Design and Workflows</a></div><i>July 21, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/A-Hands-On-Introduction-to-Conda:-July-14,-2021" target="_blank" rel="noopener" style="color:#336699;">A Hands-On Introduction to Conda</a></div><i>July 14, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <p><div style="font-size:19px"><a href="https://github.com/nih-cfde/training-and-engagement/wiki/A-Hands-On-Introduction-to-AWS:-June-30,-2021" target="_blank" rel="noopener" style="color:#336699;">Introduction to Amazon Web Services/Elastic Cloud Computing</a></div><i>June 30, 2021 • Virtual Workshop</i><br/></p> | ||
| </div> | ||
| <div> | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.