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Bioinformatics Courses

The document provides a collection of free online courses and resources for learning bioinformatics, statistics, programming languages like R and Python, and data analysis skills. These include courses from Khan Academy, Coursera, data carpentry, software carpentry, and various universities. It also lists tutorials, workshops, and books on topics such as differential expression analysis, single cell analysis, machine learning, data visualization, and population genomics. Links are provided to resources for learning R, Python, Linux commands, and data analytics tools from sources like codecademy, data mentors, software carpentry, and more.

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Tarequl Islam Nishad
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132 views

Bioinformatics Courses

The document provides a collection of free online courses and resources for learning bioinformatics, statistics, programming languages like R and Python, and data analysis skills. These include courses from Khan Academy, Coursera, data carpentry, software carpentry, and various universities. It also lists tutorials, workshops, and books on topics such as differential expression analysis, single cell analysis, machine learning, data visualization, and population genomics. Links are provided to resources for learning R, Python, Linux commands, and data analytics tools from sources like codecademy, data mentors, software carpentry, and more.

Uploaded by

Tarequl Islam Nishad
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Free online courses in Bioinformatics

Statistical learning (a great introduction by famous authors):


https://www.youtube.com/watch?v=5N9V07EIfIg&list=PLOg0ngHtcqbPTlZzRHA2ocQZqB1D_qZ5V

Khan academy offers many free courses, e.g.: https://www.khanacademy.org/math/statistics-


probability)

EMBL has a collection of courses online (with a focus on computational biology analyses):
https://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-high-throughput-
seq/differential-expression-rna-seq

Along the same lines (starts with basic concepts and then it gets more complicated; also provides R
code): http://genomicsclass.github.io/book/

Coding (general concepts, different programming languages, guided examples):


- https://www.codecademy.com ( for example: R https://www.codecademy.com/learn/learn-r,
python: https://www.codecademy.com/learn/learn-python-3)

Coursera is a great site with many online courses (https://coursera.org). Some even have guided
exercises and offer the possibility to get a certification after the completion of the course. I took this
course for Machine Learning (very easy to follow, it’s good for beginners and also has some exercises
in matlab or octave (open source)) (https://coursera.org/learn/machine-learning)

These blogs are a quick read and great for understanding how different parameters affect tSNE and
UMAP projections:
- UMAP: https://pair-code.github.io/understanding-umap/
- tSNE: https://distill.pub/2016/misread-tsne/

Differential expression analysis tools and examples:


- https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.
pdf
- understanding interactions:
http://genomicsclass.github.io/book/pages/interactions_and_contrasts.html

Single cell analysis tools and guided examples:


- https://satijalab.org/seurat/
- https://icb-scanpy.readthedocs-hosted.com/en/stable/tutorials.html

Web Seminars of Swiss Institute of Bioinformatics


https://www.youtube.com/playlist?list=PLoCxWrRWjqB1JUCntl4X09ezmOtKx1Gke

Darren Wilkinson's blog (quite computational)


https://darrenjw.wordpress.com/2010/01/30/yet-another-introduction-to-r-and-bioconductor

Learn R
#install RStudio locally, or use the free RStudio Cloud: https://rstudio.cloud/
- Basic intro: https://www.codecademy.com/learn/learn-r
- Interactive R learning with swirl: https://swirlstats.com/students.html
- Examples of main concepts: https://www.datamentor.io/r-programming/#tutorial
- R intro video: https://www.youtube.com/watch?v=_V8eKsto3Ug
- Full stats intro: https://stat545.com/index.html
- The “tidyverse” is a godsend for biologists https://www.tidyverse.org/
- R Data Science book (lots of tidyverse): https://r4ds.had.co.nz/
- Stat545 (also lots of tidyverse): https://stat545.com/
- R Graphics Cookbook: https://r-graphics.org/
- Advanced: stats learning (incl. free book): http://faculty.marshall.usc.edu/gareth-james/ISL/
- Advanced: statistical rethinking: https://github.com/rmcelreath/statrethinking_winter2019

Learn Python
- Python everything: https://chrisalbon.com/
- Basics: https://www.learnpython.org/en/Hello%2C_World%21
- Learning Biopython with coronavirus: https://github.com/chris-rands/biopython-coronavirus

Command line:
--> Beginner's guide for bash terminal: https://www.youtube.com/watch?v=oxuRxtrO2Ag
- Introduction to Linux: https://www.edx.org/course/introduction-to-linux
- Intro to Linux: https://www.guru99.com/introduction-linux.html

Data carpentry lessons: https://datacarpentry.org/lessons/


- Genomics overview: https://datacarpentry.org/genomics-workshop/
-- Command line intro for genomics: https://datacarpentry.org/shell-genomics/
-- Project organization genomics: https://datacarpentry.org/organization-genomics/

Software carpentry lessons: https://software-carpentry.org/lessons/


- R intro: http://swcarpentry.github.io/r-novice-inflammation/

General tutorial/workshop/book collections:


--> Shirley Liu STAT115 Harvard/Dana-Farber (last video in playlist is first to watch):
https://www.youtube.com/playlist?list=PLeB-Dlq-v6tY3QLdQBA7rwb4a7fK9mLpv
- Rosalind Learning Through Problem Solving: http://rosalind.info/problems/locations/
- Rosalind list of University Bioinfo Courses: http://rosalind.info/courses/
- Data Science: http://rafalab.github.io/pages/teaching.html
- Bioinformatics courses from SLU: https://www.hadriengourle.com/tutorials/
- Bioinformatics tutorials Ijaz lab: http://userweb.eng.gla.ac.uk/umer.ijaz/#bioinformatics
- Bioconductor talks/intros/workshops: https://www.bioconductor.org/help/course-materials/
- RMarkdown intro: https://ourcodingclub.github.io/tutorials/rmarkdown/
- https://kbroman.org/pages/tutorials.html
- Bioinformatics Book Pevsner lab: http://www.bioinfbook.org/
- YaleDHLab workshops: https://github.com/YaleDHLab/lab-workshops
- UMich Exploratory Data Analysis for Health (videos): https://kdpsingh.lab.medicine.umich.edu/lhs-
610
- Command line intro: https://github.com/YaleDHLab/lab-workshops/tree/master/command-line
- Jupyter Notebook workshop machine learning: https://github.com/YaleDHLab/lab-
workshops/blob/master/machine-learning/machine-learning.ipynb
- Fundamentals of data visualization: https://serialmentor.com/dataviz/index.html
- Data visualization intro: https://columbiaviz.github.io/2018f_w4995/

Data analytics:
- http://cecileane.github.io/computingtools/
- Population genomics book: https://github.com/cooplab/popgen-notes/releases/tag/v1.1
- Single-cell RNA-seq collection: https://osca.bioconductor.org/learning-r-and-more.html
- old 2011 EBI course: https://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-
high-throughput-seq/introduction-r-and-bioconductor
- Notes on data science and machine learning https://chrisalbon.com/

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