Scientific Illustrations

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93 videos

This channel is mostly about illustrations in genome biology using programming in R and Python. Based on the courses for PhD students in UMCG, University of ...

Latest Videos

A treemap. What it is and how to use it

Ternary (triangle) plot. What is it and how to read it

Coverage Plot. Multiple functions in R showing genome coverage

Descriptive statistics in ChIPpeakAnno

How I did my videos in 2025

Custom annotation in ChIPpeakAnno

DEScan2 a good alternative to DiffBind package.

UpSet plot. What it is and how to make it.

1.9.Removing duplicates from fastq files

Step Line plot as a substitute for the barplot() in R

1.8. Add your favourite Venn (Eulerr) to ChIPpeakAnno

1.7. Read and write files in loop in R

1.6. BedTools for differential analysis

1.5. Add more details to IGV

Make Venn from bed files with ChIPpeakAnno

1.4. Making average (most consistent) BED file using Bedtools

1.3. Convert BAM file into BigWig and make average tracks (of BAM files) for IGV viewer

1.2. Diffbind. What you need (BAM, BED files where to get them) and minimal protocol

1.1. Making BED files with MACS3 in python

1.0. Sort and index your BAM files using script and samtools

0.9. Visualize BAM file in IGV viewer in macOS

0.8. Fix broken fastq.gz file

0.1. An introduction to the Single Cell RNAseq

0.7. Map multiple fastq files with rsubread

0.6. Map fastq files with Rsubread

0.5. Make fastqc and multiqc reports in one python script

Happy New Year with python

0.4. Run multiQC with python

0.3. Two ways of using fastqc to generate quality report of your fastq files

0.2. Download multiple files from SRA using shell script in macOS