8-19 March 2021
By videoconference on
Day 1 / 8 March Monday / 9:00 - 17:00
Biostatistics / Statistical genetics
R-script: Basics_in_R_1.R (download and rename to remove the .txt extension)
Presentation: biostatistics course_2021
Exercises: excercises biostatistics
Day 2 / 9 March Tuesday / 9:00 - 17:00
- Exercises Day 2 & 3 -> STUDENTS-Exercises-Master2021
- Solutions -> solutions-Exercises-Master2021
- Files needed for exercises:
Protein coding genes in genomic sequences, Homology I
Homology II, Multiple sequence alignment I
Day 3 / 10 March Wednesday / 9:00 - 17:00
Multiple sequence alignment II
Seaview --> Steps:
- Download from -> seaview
- Decompress the folder
- Click on file "seaview_WINDOWS.exe"
- Go in folder "seaview"
- Click on "seaview.exe"
Day 4 / 11 March Thursday / 9:00 - 17:00
Protein structure, homology modelling
Low complexity regions / repeats
Data files: MR1_fasta
Day 5 / 12 March Friday / 9:00 - 16:30
Repeat databases / Disorder in proteins
Day 6 / 15 March Monday / 9:00 - 17:00
Introduction slides: R-Course-2021-Intro
Tutorial: click here (includes all material)
If the link to the tutorial is broken, you can use the following link to download a ZIP archive containing the tutorial and required data files: 20210310_R_tuto_ggplot
Extra exercises: click here
Day 7 / 16 March Tuesday / 14:00 - 17:00
Day 8 / 17 March Wednesday / 9:00 - 17:00
Protein interaction networks
Day 9 / 18 March Thursday / 9:00 - 17:00
Day 10 / 19 March Friday / 9:30 - 17:30
Please, install in your computer and test prior to the corresponding lesson. If you have problems installing any of the indicated software then email the corresponding contact person (in brackets).
Chimera: install current prodution release from https://www.cgl.ucsf.edu/chimera/download.html (protein 3D representation; Miguel Andrade)
JalView: install from http://www.jalview.org/getdown/release/ (alignment and structure representation; Miguel Andrade)
SeaView: (alignments and phylogenetic trees; Pablo Mier)
1. Download from: http://doua.prabi.fr/software/seaview
2. Decompress the folder
3. Click on file "seaview_WINDOWS.exe"
5. Go in folder "seaview"
6. Click on "seaview.exe"
R: (RNAseq analysis, Federico Marini) (ideally R >= 4.0.0, https://cran.r-project.org/) - latest version recommended (4.0.4 at the moment of writing)
RStudio: (RNAseq analysis, Federico Marini) (recommended)
https://rstudio.com/products/rstudio/download/, the free version is more than enough!
CRAN and Bioconductor (https://bioconductor.org/) packages: (RNAseq analysis, Federico Marini)
For the bulk transcriptome analysis:
# install the Bioc installer
# install Bioc version 3.12
BiocManager::install(version = "3.12")
# install specific Bioconductor packages
BiocManager::install(c("pcaExplorer", "ideal", "GeneTonic", "macrophage", "org.Hs.eg.db", "clusterProfiler"), dependencies = TRUE)
Check all packages are installed by calling library("package_name") e.g.
... should return no error
Cytoscape: (Protein networks; Katja Luck)
Protein Data Bank (PDB): http://www.rcsb.org/
Repeats db: http://repeatsdb.bio.unipd.it/
BLAT (UCSC): https://genome.ucsc.edu/cgi-bin/hgBlat
BLAT (UCSC european mirror): https://genome-euro.ucsc.edu/cgi-bin/hgBlatcommand=start