RBeginner

R for Bioinformatics

From the Basics to Biological Data Analysis

15 modules138 lessons15 h 50 min

No previous R or programming experience is required.

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Find what you need

Try: print, FASTA, loops, GC…

What you will learn

Understand R from zero and use it as a scientific tool.

Work with vectors, tables, missing data, and functions.

Import, clean, and visualize biological data.

Analyze DNA sequences with base R.

Understand what Bioconductor is for and how it is organized.

Build a reproducible biological-data report.

Your path

0. Welcome to R

30 min · 0/7

0.1 · What is R?0.2 · Why scientists use R0.3 · Meet the R console0.4 · Your first R calculation+3

1. Your First Objects

50 min · 0/9

1.1 · R as a calculator1.2 · Saving a value with <-1.3 · Object names1.4 · Numbers+5

2. Vectors: R's Superpower

1 h · 0/10

2.1 · What is a vector?2.2 · Create a vector with c()2.3 · Vector arithmetic2.4 · How long is a vector?+6

3. Selecting the Data You Need

50 min · 0/8

3.1 · R starts counting at 13.2 · Select one position3.3 · Select several positions3.4 · Remove values with negative indices+4

4. Ways to Organize Data

1 h · 0/9

4.1 · Vectors have one dimension4.2 · Matrices are grids4.3 · Rows and columns4.4 · Summarize a matrix+5

5. Data Frames: Organizing Biological Data

1 h 5 min · 0/10

5.1 · What is a data frame?5.2 · Create a data frame5.3 · Look inside with str()5.4 · Preview with head()+6

6. Questions, Decisions, and Missing Data

50 min · 0/8

6.1 · Comparisons return logical values6.2 · Make decisions with if6.3 · Handle alternatives with else6.4 · Make vectorized decisions with ifelse()+4

7. Repeat Smartly: Vectorization and Loops

1 h · 0/9

7.1 · R works naturally with vectors7.2 · Vectorize a calculation7.3 · Vectorized decisions7.4 · Your first for loop+5

8. Build Your Own Functions

1 h 5 min · 0/9

8.1 · Why functions exist8.2 · Create a function8.3 · Pass an argument to a function8.4 · Return a result+5

9. Import and Clean Biological Data

1 h 5 min · 0/9

9.1 · What is a CSV file?9.2 · Read CSV text9.3 · What is a TSV file?9.4 · Read tab-separated data+5

10. Visualizing Biological Data

1 h 10 min · 0/9

10.1 · Why make a graph?10.2 · Your first plot()10.3 · Label axes10.4 · Bar plots+5

11. DNA, Proteins, and FASTA in R

1 h 25 min · 0/14

11.1 · A DNA sequence is text11.2 · Measure sequence length11.3 · Split DNA into bases11.4 · Count nucleotides+10

12. Bioconductor Without Fear

1 h 15 min · 0/9

12.1 · What is Bioconductor?12.2 · Packages are toolboxes12.3 · Installing packages with BiocManager12.4 · Meet Biostrings+5

13. Final Project: Biological Data Report

1 h 20 min · 0/8

13.1 · Understand the question13.2 · Build the sample table13.3 · Validate the data13.4 · Create reusable functions+4

14. From Data to Paper: Publication-Ready Figures

1 h 25 min · 0/10

14.1 · A figure is a scientific argument14.2 · Meet ggplot2: data + mapping + geometry14.3 · Show the real observations14.4 · Color that still works when color disappears+6