Scientific Illustrations

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 Groningen

UpSet plot. What it is and how to make it.
UpSet plot. What it is and how to make it.
1.9.Removing duplicates from fastq files
1.9.Removing duplicates from fastq files
Step Line plot as a substitute for the barplot() in R
Step Line plot as a substitute for the barplot() in R
1.8. Add your favourite Venn (Eulerr) to ChIPpeakAnno
1.8. Add your favourite Venn (Eulerr) to ChIPpeakAnno
1.7. Read and write files in loop in R
1.7. Read and write files in loop in R
1.6. BedTools for differential analysis?
1.6. BedTools for differential analysis?
1.5. Add more details to IGV
1.5. Add more details to IGV
Make Venn from bed files with ChIPpeakAnno
Make Venn from bed files with ChIPpeakAnno
1.4. Making average (most consistent) BED file using Bedtools
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
1.3. 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
1.2. Diffbind. What you need (BAM, BED files: where to get them) and minimal protocol
1.1. Making BED files with MACS3 in python
1.1. Making BED files with MACS3 in python
1.0. Sort and index your BAM files using script and samtools
1.0. Sort and index your BAM files using script and samtools
0.9. Visualize BAM file in IGV viewer in macOS
0.9. Visualize BAM file in IGV viewer in macOS
0.8. Fix broken fastq.gz file
0.8. Fix broken fastq.gz file
0.1. An introduction to the Single Cell RNAseq
0.1. An introduction to the Single Cell RNAseq
0.7. Map multiple fastq files with rsubread
0.7. Map multiple fastq files with rsubread
0.6. Map fastq files with Rsubread
0.6. Map fastq files with Rsubread
0.5. Make fastqc and multiqc reports in one python script
0.5. Make fastqc and multiqc reports in one python script
Happy New Year with python
Happy New Year with python
0.4. Run multiQC with python
0.4. Run multiQC with python
0.3. Two ways of using fastqc to generate quality report of your fastq files
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
0.2. Download multiple files from SRA using shell script in macOS
0.1. FASTQ from NCBI SRA
0.1. FASTQ from NCBI SRA
1.11. CEL files in limma GEO2R script
1.11. CEL files in limma GEO2R script
1.10. Multiple groups and contrasts in limma
1.10. Multiple groups and contrasts in limma
3.3. Time in DESeq2
3.3. Time in DESeq2
6.1. Convert your Rmd script into a good looking report
6.1. Convert your Rmd script into a good looking report
3.2. Using time (age) scale in limma
3.2. Using time (age) scale in limma
3.1. edgeR with real age and gender. Will it work?
3.1. edgeR with real age and gender. Will it work?