Coding and machine learning

MATLAB Onramp - free with a University email addression content

Microbiome Discovery - a YouTube lecture series on microbial community data analysis

Intro to Python - a Microsoft course

Python for Beginners - a wide selection of YouTube videos

A Beginner's Guide to R - an e-book that can be downloaded as a series of PDF chapters

Swirl - Swirl teaches you R programming and data science interactively at your own pace

RNAseq analysis in R - a workshop on analysing RNA-seq count data, using R

Bulk RNA-seq

STAR aligner - this is commonly used to map the reads to the genome reference

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The links below are for DESeq2, possibly the most commonly used R package for differential expression analysis:

Analyzing RNA-seq data with DESeq2

RNA-seq workflow: gene-level exploratory analysis and differential expression

 

Single cell RNA-seq

Current Best Practices in Single-Cell RNA-seq Analysis - a recently published tutorial

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10x Genomics provides Cell Ranger software for 10x Chromium data processing and Loupe Cell Browser for data visualisation and simple analysis:

What is Cell Ranger? and Getting Started with Cell Ranger

What is Loupe Browser? and Loupe Browser Tutorial

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Seurat package in R is commonly used for more sophisticated analysis and has many tutorials available. The tutorials below are particularly useful to start with:

Differential expression testing

Guided Clustering Tutorial

Introduction to Slurm

Cognitive Class - free courses focusing on data science and cognitive computing

LinkedIn Learning - use the link on this page to login with a University email address

Software Carpentry - teaches basic lab skills for research computing, including Unix, Git, Python and R