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https://github.com/mahshaaban/intro_data_r

A gentle introduction to data analysis in R
https://github.com/mahshaaban/intro_data_r

data-analysis image-analysis qpcr-analysis r

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A gentle introduction to data analysis in R

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## Introduction to data analysis in R

### Description

This is a short course on data analysis in R. The goal is to get the
participants familiar with R code and to appreciate it as a tool to handle
common experimental data. The materials are delivered in the form of
lectures and interactive exercises.

### Objectives

- To get familiar with R as a tool for data analysis
- To apply basic arithmetic and statistics in R
- To learn to handle experimental data in R (qPCR and images)

### Format

Each module is delivered in three steps

- [`lectures/`](lectures/): slides discussing the main concepts
- [`practice/`](practice/): interactive exercises for practicing purposes
- [`homework/`](homework/): more exercises to test understanding

### Outline

- Getting started in R
- Lecture ([Slides](lectures/lecture_1.pdf))
- Practice ([Link](https://bcmslab.shinyapps.io/practice_1/))
- Homework ([Link](https://bcmslab.shinyapps.io/homework_1/))
- Basic statistics in R
- Lecture ([Slides](lectures/lecture_2.pdf))
- Practice ([Link](https://bcmslab.shinyapps.io/practice_2/))
- Homework ([Link](https://bcmslab.shinyapps.io/homework_2/))
- Quantifying mRNA using the `pcr` package
- Lecture ([Slides](lectures/lecture_3.pdf))
- Practice ([Link](https://bcmslab.shinyapps.io/practice_3/))
- Homework ([Link](https://bcmslab.shinyapps.io/homework_3/))
- Quantifying protein co-localization in fluorescence images using the `colocr` package
- Lecture ([Slides](lectures/lecture_4.pdf))
- Practice ([Link](https://bcmslab.shinyapps.io/practice_4/))
- Homework ([Link](https://bcmslab.shinyapps.io/homework_4/))

### Readings

- Tidy data by Hadley Wickham ([Link](https://www.jstatsoft.org/article/view/v059i10))
- Ahmed M, Kim DR. pcr: an R package for quality assessment, analysis and
testing of qPCR data. PeerJ. 2018 Mar 16;6:e4473.
doi: [10.7717/peerj.4473](https://pubmed.ncbi.nlm.nih.gov/29576953/).
- Ahmed M, Lai TH, Kim DR. colocr: an R package for conducting co-localization
analysis on fluorescence microscopy images. PeerJ. 2019;7:e7255.
doi:[10.7717/peerj.7255](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612416/)

### Resources (what to learn next?)

- Introduction to R ([Data Camp Free Interactive Course](https://www.datacamp.com/courses/free-introduction-to-r))
- Intermediate R Course ([Data Camp Free Interactive Course](https://www.datacamp.com/courses/intermediate-r))
- R for Data Science ([Book](https://www.amazon.co.jp/-/en/Hadley-Wickham/dp/1491910399))