<commit_before>---
layout: page
title: External Training Courses
excerpt: "Details of courses and resources from other providers"
---

# Training from External Providers

We have compiled this link of recommended materials from other providers, and materials developed in previous roles.

## Youtube Playlists

- [<NAME> learning](https://www.youtube.com/channel/UC7aizSyonJqZI3O3U4SDTiA/videos)
- [Babraham Bioinformatics Bitesize videos](https://www.youtube.com/playlist?list=PLbiByRpDb_hP7b-I1GR4eEWCD2OqdZEg1)
- [<NAME>](https://www.youtube.com/user/RafalabChannel/videos)
- [<NAME> - Algorithms for DNA Sequencing](https://www.youtube.com/watch?v=hpb-mH-yjLc&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA)
- [Bioconductor playlists](https://www.youtube.com/user/bioconductor/playlists)
- [<NAME> - Exploratory Data Analysis](https://www.youtube.com/watch?v=6lOvA_y7p7w&list=PLjTlxb-wKvXPhZ7tQwlROtFjorSj9tUyZ)

## Reproducible Research / Data Management

### Materials

- [Reproducible Research Data and Project Management in R](https://annakrystalli.me/rrresearchACCE20/)
- [The Data Organisation Tutorial by <NAME>](http://kbroman.org/dataorg/)
- [The Quartz guide to bad data](https://github.com/Quartz/bad-data-guide/blob/master/README.md)
- [Three common bad practices in sharing tables and spreadsheets and how to avoid them](http://luisdva.github.io/pls-don't-do-this/)
- [Biologists: this is why bioinformaticians hate you…](http://www.opiniomics.org/biologists-this-is-why-bioinformaticians-hate-you/)

### Videos

- [<NAME> lecture on reproducible research](https://youtu.be/7gYIs7uYbMo)
- [<NAME> - Five Selfish Reasons to Work Reproducibly](https://www.youtube.com/watch?v=1Y_oIjlH-yg)
- [<NAME> - Show your working](https://youtu.be/e-7Pfi_bGaE)

## RNA-seq

### Course Materials

- [University of York Differential Gene Expression Tutorial](https://shiny.york.ac.uk/bioltf/gene_expression_course/day1/)
- [Harvard Bioinformatics Core Differential gene expression](https://hbctraining.github.io/DGE_workshop_salmon/)
- 
### Videos

- [RPKM / FPKM explained](https://www.youtube.com/watch?v=TTUrtCY2k-w&t=543s)

## Version control / git and github

- [Software Carpentry git Lessons](http://swcarpentry.github.io/git-novice/)
- [Github Guides](https://guides.github.com/)

## ChiP-seq / ATAC-seq

- [Harvard Bioinformatics Core ChIP-seq training](https://hbctraining.github.io/Intro-to-ChIPseq/)
- [Rockefeller Bioinformatics](https://rockefelleruniversity.github.io/RU_ChIPseq/)
- [Rockefeller Bioinformatics](https://rockefelleruniversity.github.io/RU_ATACseq/)

## Single-cell RNA-seq

### Course Materials

- [Analysis of single cell RNA-seq data - Sanger](https://scrnaseq-course.cog.sanger.ac.uk/website/index.html)
- [Analysis of single cell RNA-seq data - Harvard Bioinformatics Core](https://hbctraining.github.io/scRNA-seq/)

### Videos

- [Analysis of single cell RNA-seq data - Day 1](https://youtu.be/thHgPqQpkE4)
- [Analysis of single cell RNA-seq data - Day 2](https://youtu.be/7dQ_pleDO2Y)

## Cancer Genomics

- [CRUK Bioinformatics Summer School](https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/)

## Functional Genomics (RNA- and ChIP-seq)

- [CRUK Autumn School](https://bioinformatics-core-shared-training.github.io/cruk-autumn-school-2017/)

## Python Programming

- [Software Carpentry Programming with Python](https://swcarpentry.github.io/python-novice-inflammation/)
- [Solving biological problems with Python
](http://pycam.github.io/)

## Experimental Design

- [CRUK course on Experimental Design](http://bioinformatics-core-shared-training.github.io/experimental-design/)

## Microarray Analysis

- [CRUK course on microarray analysis](http://bioinformatics-core-shared-training.github.io/microarray-analysis/)

## Shiny (R)

- [CRUK course on Shiny for Bioinformatics](https://bioinformatics-core-shared-training.github.io/shiny-bioinformatics/)

## Docker

- [CRUK course on using Docker](http://bioinformatics-core-shared-training.github.io/docker-4-bioinformatics/)

## Linear Models in R

- [CRUK Linear Models course](http://tinyurl.com/linear-models-r)

# Training Portals

- [Galaxy Training Network](https://galaxyproject.org/teach/gtn/)
- [GOBLET training portal](https://www.mygoblet.org/training-portal)<commit_msg>Update other-materials.md<commit_after>---
layout: page
title: External Training Courses
excerpt: "Details of courses and resources from other providers"
---

# Training from External Providers

We have compiled this link of recommended materials from other providers, and materials developed in previous roles.

## Youtube Playlists

- [<NAME> Lockdown learning](https://www.youtube.com/channel/UC7aizSyonJqZI3O3U4SDTiA/videos)
- [Babraham Bioinformatics Bitesize videos](https://www.youtube.com/playlist?list=PLbiByRpDb_hP7b-I1GR4eEWCD2OqdZEg1)
- [<NAME>](https://www.youtube.com/user/RafalabChannel/videos)
- [<NAME> - Algorithms for DNA Sequencing](https://www.youtube.com/watch?v=hpb-mH-yjLc&list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA)
- [Bioconductor playlists](https://www.youtube.com/user/bioconductor/playlists)
- [<NAME> - Exploratory Data Analysis](https://www.youtube.com/watch?v=6lOvA_y7p7w&list=PLjTlxb-wKvXPhZ7tQwlROtFjorSj9tUyZ)

## Reproducible Research / Data Management

### Materials

- [Reproducible Research Data and Project Management in R](https://annakrystalli.me/rrresearchACCE20/)
- [The Data Organisation Tutorial by <NAME>](http://kbroman.org/dataorg/)
- [The Quartz guide to bad data](https://github.com/Quartz/bad-data-guide/blob/master/README.md)
- [Three common bad practices in sharing tables and spreadsheets and how to avoid them](http://luisdva.github.io/pls-don't-do-this/)
- [Biologists: this is why bioinformaticians hate you…](http://www.opiniomics.org/biologists-this-is-why-bioinformaticians-hate-you/)

### Videos

- [<NAME> lecture on reproducible research](https://youtu.be/7gYIs7uYbMo)
- [<NAME> - Five Selfish Reasons to Work Reproducibly](https://www.youtube.com/watch?v=1Y_oIjlH-yg)
- [<NAME> - Show your working](https://youtu.be/e-7Pfi_bGaE)

## Unix / Command Line

- [Babraham Bioinformatics](https://www.bioinformatics.babraham.ac.uk/training.html#unix)
- [Software Carpentry](https://swcarpentry.github.io/shell-novice/)
- [CRUK Command Line for Genomics](https://bioinformatics-core-shared-training.github.io/shell-genomics/)


## RNA-seq

### Course Materials

- [University of York Differential Gene Expression Tutorial](https://shiny.york.ac.uk/bioltf/gene_expression_course/day1/)
- [Harvard Bioinformatics Core Differential gene expression](https://hbctraining.github.io/DGE_workshop_salmon/)
- 
### Videos

- [RPKM / FPKM explained](https://www.youtube.com/watch?v=TTUrtCY2k-w&t=543s)

## Version control / git and github

- [Software Carpentry git Lessons](http://swcarpentry.github.io/git-novice/)
- [Github Guides](https://guides.github.com/)

## ChiP-seq / ATAC-seq

- [Harvard Bioinformatics Core ChIP-seq training](https://hbctraining.github.io/Intro-to-ChIPseq/)
- [Rockefeller Bioinformatics](https://rockefelleruniversity.github.io/RU_ChIPseq/)
- [Rockefeller Bioinformatics](https://rockefelleruniversity.github.io/RU_ATACseq/)
- [Babraham Bioinformatis](https://www.bioinformatics.babraham.ac.uk/training.html#chip)

## Single-cell RNA-seq

### Course Materials

- [Analysis of single cell RNA-seq data - Sanger](https://scrnaseq-course.cog.sanger.ac.uk/website/index.html)
- [Analysis of single cell RNA-seq data - Harvard Bioinformatics Core](https://hbctraining.github.io/scRNA-seq/)
- [10X analysis - Babraham Bioinformatics](https://www.bioinformatics.babraham.ac.uk/training.html#10xrna)

### Videos

- [Analysis of single cell RNA-seq data - Day 1](https://youtu.be/thHgPqQpkE4)
- [Analysis of single cell RNA-seq data - Day 2](https://youtu.be/7dQ_pleDO2Y)

## Cancer Genomics

- [CRUK Bioinformatics Summer School](https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/)

## Functional Genomics (RNA- and ChIP-seq)

- [CRUK Autumn School](https://bioinformatics-core-shared-training.github.io/cruk-autumn-school-2017/)

## Python Programming

- [Software Carpentry Programming with Python](https://swcarpentry.github.io/python-novice-inflammation/)
- [Solving biological problems with Python
](http://pycam.github.io/)

## Experimental Design

- [CRUK course on Experimental Design](http://bioinformatics-core-shared-training.github.io/experimental-design/)

## Microarray Analysis

- [CRUK course on microarray analysis](http://bioinformatics-core-shared-training.github.io/microarray-analysis/)

## Shiny (R)

- [CRUK course on Shiny for Bioinformatics](https://bioinformatics-core-shared-training.github.io/shiny-bioinformatics/)

## Docker

- [CRUK course on using Docker](http://bioinformatics-core-shared-training.github.io/docker-4-bioinformatics/)

## Statistics in R

- [CRUK Linear Models course](http://tinyurl.com/linear-models-r)
- [Babraham Bioinformatics Statistics in R](https://www.bioinformatics.babraham.ac.uk/training.html#rstats)

# Scientific Figure Design

- [Babraham Bioinformatics](https://www.bioinformatics.babraham.ac.uk/training.html#figuredesign)


# Training Portals

- [Galaxy Training Network](https://galaxyproject.org/teach/gtn/)
- [GOBLET training portal](https://www.mygoblet.org/training-portal)
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