A Tidy Transcriptomics introduction to RNA-Seq analyses
This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.
Scientific topics: RNA-Seq
Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics
Resource type: Tutorial
A Tidy Transcriptomics introduction to RNA-Seq analyses
https://stemangiola.github.io/bioc_2020_tidytranscriptomics/
http://tess.elixir-uk.org/materials/a-tidy-transcriptomics-introduction-to-rna-seq-analyses
This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.
Maria Doyle
Stefano Mangiola
RNA-Seq
Differential Expression, Gene Expression, RNA-seq, Transcriptomics
Biologists
Big Data, Genes, and Medicine
This course distills for you expert knowledge and skills mastered by professionals in Health Big Data Science and Bioinformatics. You will learn exciting facts about the human body biology and chemistry, genetics, and medicine that will be intertwined with the science of Big Data and skills to...
Keywords: life-sciences, computer-science, bioinformatics, algorithms
Big Data, Genes, and Medicine
https://www.coursera.org/learn/data-genes-medicine
http://tess.elixir-uk.org/materials/big-data-genes-and-medicine
This course distills for you expert knowledge and skills mastered by professionals in Health Big Data Science and Bioinformatics. You will learn exciting facts about the human body biology and chemistry, genetics, and medicine that will be intertwined with the science of Big Data and skills to harness the avalanche of data openly available at your fingertips and which we are just starting to make sense of. We’ll investigate the different steps required to master Big Data analytics on real datasets, including Next Generation Sequencing data, in a healthcare and biological context, from preparing data for analysis to completing the analysis, interpreting the results, visualizing them, and sharing the results.
Needless to say, when you master these high-demand skills, you will be well positioned to apply for or move to positions in biomedical data analytics and bioinformatics. No matter what your skill levels are in biomedical or technical areas, you will gain highly valuable new or sharpened skills that will make you stand-out as a professional and want to dive even deeper in biomedical Big Data. It is my hope that this course will spark your interest in the vast possibilities offered by publicly available Big Data to better understand, prevent, and treat diseases.
life-sciences, computer-science, bioinformatics, algorithms
2017-03-24
Bioinformatics Capstone: Big Data in Biology
In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.
In particular, in a series of Application Challenges will see how genome assembly can be used...
Keywords: life-sciences, computer-science, health-informatics, algorithms
Bioinformatics Capstone: Big Data in Biology
https://www.coursera.org/learn/bioinformatics-project
http://tess.elixir-uk.org/materials/bioinformatics-capstone-big-data-in-biology
In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.
In particular, in a series of Application Challenges will see how genome assembly can be used to track the source of a food poisoning outbreak, how RNA-Sequencing can help us analyze gene expression data on the tissue level, and compare the pros and cons of whole genome vs. whole exome sequencing for finding potentially harmful mutations in a human sample.
Plus, hacker track students will have the option to build their own genome assembler and apply it to real data!
life-sciences, computer-science, health-informatics, algorithms
2017-03-25
Functional genomics (III): Submitting your data and functional genomics databases
Functional genomics (III): Submitting your data and functional genomics databases from http://www.ebi.ac.uk/training/online/course/functional-genomics-iii-submitting-your-data-and-f.
Keywords: Gene Expression
Functional genomics (III): Submitting your data and functional genomics databases
http://www.ebi.ac.uk/training/online/course/functional-genomics-iii-submitting-your-data-and-f
http://tess.elixir-uk.org/materials/functional-genomics-iii-submitting-your-data-and-functional-genomics-databases
Functional genomics (III): Submitting your data and functional genomics databases from http://www.ebi.ac.uk/training/online/course/functional-genomics-iii-submitting-your-data-and-f.
Gene Expression
2016-06-14
Functional genomics (I): Introduction and designing experiments
Functional genomics (I): Introduction and designing experiments from http://www.ebi.ac.uk/training/online/course/functional-genomics-i-introduction-and-designing-e.
Keywords: Gene Expression
Functional genomics (I): Introduction and designing experiments
http://www.ebi.ac.uk/training/online/course/functional-genomics-i-introduction-and-designing-e
http://tess.elixir-uk.org/materials/functional-genomics-i-introduction-and-designing-experiments
Functional genomics (I): Introduction and designing experiments from http://www.ebi.ac.uk/training/online/course/functional-genomics-i-introduction-and-designing-e.
Gene Expression
2016-06-14
Finding Hidden Messages in DNA (Bioinformatics I)
Named a top 50 MOOC of all time by Class Central!
This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat.
In the first half of the...
Keywords: life-sciences, computer-science, health-informatics, algorithms
Finding Hidden Messages in DNA (Bioinformatics I)
https://www.coursera.org/learn/dna-analysis
http://tess.elixir-uk.org/materials/finding-hidden-messages-in-dna-bioinformatics-i
Named a top 50 MOOC of all time by Class Central!
This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat.
In the first half of the course, we investigate DNA replication, and ask the question, where in the genome does DNA replication begin? We will see that we can answer this question for many bacteria using only some straightforward algorithms to look for hidden messages in the genome.
In the second half of the course, we examine a different biological question, when we ask which DNA patterns play the role of molecular clocks. The cells in your body manage to maintain a circadian rhythm, but how is this achieved on the level of DNA? Once again, we will see that by knowing which hidden messages to look for, we can start to understand the amazingly complex language of DNA. Perhaps surprisingly, we will apply randomized algorithms, which roll dice and flip coins in order to solve problems.
Finally, you will get your hands dirty and apply existing software tools to find recurring biological motifs within genes that are responsible for helping Mycobacterium tuberculosis go "dormant" within a host for many years before causing an active infection.
life-sciences, computer-science, health-informatics, algorithms
2017-10-09
Finding Mutations in DNA and Proteins (Bioinformatics VI)
In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins.
In the first half of the course, we would like to ask how an individual's genome differs from the...
Keywords: life-sciences, computer-science, health-informatics, algorithms
Finding Mutations in DNA and Proteins (Bioinformatics VI)
https://www.coursera.org/learn/dna-mutations
http://tess.elixir-uk.org/materials/finding-mutations-in-dna-and-proteins-bioinformatics-vi
In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins.
In the first half of the course, we would like to ask how an individual's genome differs from the "reference genome" of the species. Our goal is to take small fragments of DNA from the individual and "map" them to the reference genome. We will see that the combinatorial pattern matching algorithms solving this problem are elegant and extremely efficient, requiring a surprisingly small amount of runtime and memory.
In the second half of the course, we will learn how to identify the function of a protein even if it has been bombarded by so many mutations compared to similar proteins with known functions that it has become barely recognizable. This is the case, for example, in HIV studies, since the virus often mutates so quickly that researchers can struggle to study it. The approach we will use is based on a powerful machine learning tool called a hidden Markov model.
Finally, you will learn how to apply popular bioinformatics software tools applying hidden Markov models to compare a protein against a related family of proteins.
life-sciences, computer-science, health-informatics, algorithms
2017-10-09
Genome Sequencing (Bioinformatics II)
You may have heard a lot about genome sequencing and its potential to usher in an era of personalized medicine, but what does it mean to sequence a genome?
Biologists still cannot read the nucleotides of an entire genome as you would read a book from beginning to end. However, they can read...
Keywords: life-sciences, computer-science, health-informatics, algorithms
Genome Sequencing (Bioinformatics II)
https://www.coursera.org/learn/genome-sequencing
http://tess.elixir-uk.org/materials/genome-sequencing-bioinformatics-ii
You may have heard a lot about genome sequencing and its potential to usher in an era of personalized medicine, but what does it mean to sequence a genome?
Biologists still cannot read the nucleotides of an entire genome as you would read a book from beginning to end. However, they can read short pieces of DNA. In this course, we will see how graph theory can be used to assemble genomes from these short pieces. We will further learn about brute force algorithms and apply them to sequencing mini-proteins called antibiotics.
In the first half of the course, we will see that biologists cannot read the 3 billion nucleotides of a human genome as you would read a book from beginning to end. However, they can read shorter fragments of DNA. In this course, we will see how graph theory can be used to assemble genomes from these short pieces in what amounts to the largest jigsaw puzzle ever put together.
In the second half of the course, we will discuss antibiotics, a topic of great relevance as antimicrobial-resistant bacteria like MRSA are on the rise. You know antibiotics as drugs, but on the molecular level they are short mini-proteins that have been engineered by bacteria to kill their enemies. Determining the sequence of amino acids making up one of these antibiotics is an important research problem, and one that is similar to that of sequencing a genome by assembling tiny fragments of DNA. We will see how brute force algorithms that try every possible solution are able to identify naturally occurring antibiotics so that they can be synthesized in a lab.
Finally, you will learn how to apply popular bioinformatics software tools to sequence the genome of a deadly Staphylococcus bacterium that has acquired antibiotics resistance.
life-sciences, computer-science, health-informatics, algorithms
2017-10-09
Biology Meets Programming: Bioinformatics for Beginners
Are you interested in learning how to program (in Python) within a scientific setting?
This course will cover algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms in Python. It offers a gently-paced introduction...
Keywords: life-sciences, computer-science, health-informatics, software-development
Biology Meets Programming: Bioinformatics for Beginners
https://www.coursera.org/learn/bioinformatics
http://tess.elixir-uk.org/materials/biology-meets-programming-bioinformatics-for-beginners
Are you interested in learning how to program (in Python) within a scientific setting?
This course will cover algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms in Python. It offers a gently-paced introduction to our Bioinformatics Specialization (https://www.coursera.org/specializations/bioinformatics), preparing learners to take the first course in the Specialization, "Finding Hidden Messages in DNA" (https://www.coursera.org/learn/dna-analysis).
Each of the four weeks in the course will consist of two required components. First, an interactive textbook provides Python programming challenges that arise from real biological problems. If you haven't programmed in Python before, not to worry! We provide "Just-in-Time" exercises from the Codecademy Python track (https://www.codecademy.com/learn/python). And each page in our interactive textbook has its own discussion forum, where you can interact with other learners. Second, each week will culminate in a summary quiz.
Lecture videos are also provided that accompany the material, but these videos are optional.
life-sciences, computer-science, health-informatics, software-development
2017-05-04
Genomic Data Science and Clustering (Bioinformatics V)
How do we infer which genes orchestrate various processes in the cell? How did humans migrate out of Africa and spread around the world? In this class, we will see that these two seemingly different questions can be addressed using similar algorithmic and machine learning techniques arising from...
Keywords: life-sciences, computer-science, health-informatics, algorithms
Genomic Data Science and Clustering (Bioinformatics V)
https://www.coursera.org/learn/genomic-data
http://tess.elixir-uk.org/materials/genomic-data-science-and-clustering-bioinformatics-v
How do we infer which genes orchestrate various processes in the cell? How did humans migrate out of Africa and spread around the world? In this class, we will see that these two seemingly different questions can be addressed using similar algorithmic and machine learning techniques arising from the general problem of dividing data points into distinct clusters.
In the first half of the course, we will introduce algorithms for clustering a group of objects into a collection of clusters based on their similarity, a classic problem in data science, and see how these algorithms can be applied to gene expression data.
In the second half of the course, we will introduce another classic tool in data science called principal components analysis that can be used to preprocess multidimensional data before clustering in an effort to greatly reduce the number dimensions without losing much of the "signal" in the data.
Finally, you will learn how to apply popular bioinformatics software tools to solve a real problem in clustering.
life-sciences, computer-science, health-informatics, algorithms
2017-10-09
Comparing Genes, Proteins, and Genomes (Bioinformatics III)
Once we have sequenced genomes in the previous course, we would like to compare them to determine how species have evolved and what makes them different.
In the first half of the course, we will compare two short biological sequences, such as genes (i.e., short sequences of DNA) or proteins. We...
Keywords: life-sciences, computer-science, health-informatics, algorithms
Comparing Genes, Proteins, and Genomes (Bioinformatics III)
https://www.coursera.org/learn/comparing-genomes
http://tess.elixir-uk.org/materials/comparing-genes-proteins-and-genomes-bioinformatics-iii
Once we have sequenced genomes in the previous course, we would like to compare them to determine how species have evolved and what makes them different.
In the first half of the course, we will compare two short biological sequences, such as genes (i.e., short sequences of DNA) or proteins. We will encounter a powerful algorithmic tool called dynamic programming that will help us determine the number of mutations that have separated the two genes/proteins.
In the second half of the course, we will "zoom out" to compare entire genomes, where we see large scale mutations called genome rearrangements, seismic events that have heaved around large blocks of DNA over millions of years of evolution. Looking at the human and mouse genomes, we will ask ourselves: just as earthquakes are much more likely to occur along fault lines, are there locations in our genome that are "fragile" and more susceptible to be broken as part of genome rearrangements? We will see how combinatorial algorithms will help us answer this question.
Finally, you will learn how to apply popular bioinformatics software tools to solve problems in sequence alignment, including BLAST.
life-sciences, computer-science, health-informatics, algorithms
2017-10-09
Molecular Evolution (Bioinformatics IV)
In the previous course in the Specialization, we learned how to compare genes, proteins, and genomes. One way we can use these methods is in order to construct a "Tree of Life" showing how a large collection of related organisms have evolved over time.
In the first half of the course, we will...
Keywords: life-sciences, computer-science, health-informatics, algorithms
Molecular Evolution (Bioinformatics IV)
https://www.coursera.org/learn/molecular-evolution
http://tess.elixir-uk.org/materials/molecular-evolution-bioinformatics-iv
In the previous course in the Specialization, we learned how to compare genes, proteins, and genomes. One way we can use these methods is in order to construct a "Tree of Life" showing how a large collection of related organisms have evolved over time.
In the first half of the course, we will discuss approaches for evolutionary tree construction that have been the subject of some of the most cited scientific papers of all time, and show how they can resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans.
In the second half of the course, we will shift gears and examine the old claim that birds evolved from dinosaurs. How can we prove this? In particular, we will examine a result that claimed that peptides harvested from a T. rex fossil closely matched peptides found in chickens. In particular, we will use methods from computational proteomics to ask how we could assess whether this result is valid or due to some form of contamination.
Finally, you will learn how to apply popular bioinformatics software tools to reconstruct an evolutionary tree of ebolaviruses and identify the source of the recent Ebola epidemic that caused global headlines.
life-sciences, computer-science, health-informatics, algorithms
2017-10-09
ArrayExpress: Discover functional genomics data quickly and easily
ArrayExpress: Discover functional genomics data quickly and easily from http://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui.
Keywords: Gene Expression
ArrayExpress: Discover functional genomics data quickly and easily
http://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui
http://tess.elixir-uk.org/materials/arrayexpress-discover-functional-genomics-data-quickly-and-easily
ArrayExpress: Discover functional genomics data quickly and easily from http://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui.
Gene Expression
2016-06-14
Functional genomics: An introduction to EMBL-EBI resources
Functional genomics: An introduction to EMBL-EBI resources from http://www.ebi.ac.uk/training/online/course/functional-genomics-introduction-embl-ebi-resource-1.
Keywords: Gene Expression
Functional genomics: An introduction to EMBL-EBI resources
http://www.ebi.ac.uk/training/online/course/functional-genomics-introduction-embl-ebi-resource-1
http://tess.elixir-uk.org/materials/functional-genomics-an-introduction-to-embl-ebi-resources
Functional genomics: An introduction to EMBL-EBI resources from http://www.ebi.ac.uk/training/online/course/functional-genomics-introduction-embl-ebi-resource-1.
Gene Expression
2016-06-14
Expression Atlas: Quick tour
Expression Atlas: Quick tour from http://www.ebi.ac.uk/training/online/course/expression-atlas-quick-tour-0.
Keywords: Gene Expression
Expression Atlas: Quick tour
http://www.ebi.ac.uk/training/online/course/expression-atlas-quick-tour-0
http://tess.elixir-uk.org/materials/expression-atlas-quick-tour
Expression Atlas: Quick tour from http://www.ebi.ac.uk/training/online/course/expression-atlas-quick-tour-0.
Gene Expression
2016-06-14
EMBO Practical Course on Analysis of High-Throughput Sequencing Data
EMBO Practical Course on Analysis of High-Throughput Sequencing Data from http://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-high-throughput-seq.
Keywords: Gene Expression
EMBO Practical Course on Analysis of High-Throughput Sequencing Data
http://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-high-throughput-seq
http://tess.elixir-uk.org/materials/embo-practical-course-on-analysis-of-high-throughput-sequencing-data
EMBO Practical Course on Analysis of High-Throughput Sequencing Data from http://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-high-throughput-seq.
Gene Expression
2016-06-14
EBI: Next Generation Sequencing Practical Course
EBI: Next Generation Sequencing Practical Course from http://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course.
Scientific topics: Sequencing
Keywords: DNA RNA, Gene Expression
EBI: Next Generation Sequencing Practical Course
http://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course
http://tess.elixir-uk.org/materials/ebi-next-generation-sequencing-practical-course
EBI: Next Generation Sequencing Practical Course from http://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course.
Sequencing
DNA RNA, Gene Expression
2016-06-14
diXa data warehouse: Exploring data from toxicogenomics studies
diXa data warehouse: Exploring data from toxicogenomics studies from http://www.ebi.ac.uk/training/online/course/dixa-data-warehouse-exploring-data-toxicogenomics.
Keywords: Gene Expression, Ontologies, Chemical biology
diXa data warehouse: Exploring data from toxicogenomics studies
http://www.ebi.ac.uk/training/online/course/dixa-data-warehouse-exploring-data-toxicogenomics
http://tess.elixir-uk.org/materials/dixa-data-warehouse-exploring-data-from-toxicogenomics-studies
diXa data warehouse: Exploring data from toxicogenomics studies from http://www.ebi.ac.uk/training/online/course/dixa-data-warehouse-exploring-data-toxicogenomics.
Gene Expression, Ontologies, Chemical biology
2016-06-14
BioSamples: Quick tour
BioSamples: Quick tour from http://www.ebi.ac.uk/training/online/course/biosamples-quick-tour.
Keywords: DNA RNA, Gene Expression, Ontologies, Proteins
BioSamples: Quick tour
http://www.ebi.ac.uk/training/online/course/biosamples-quick-tour
http://tess.elixir-uk.org/materials/biosamples-quick-tour
BioSamples: Quick tour from http://www.ebi.ac.uk/training/online/course/biosamples-quick-tour.
DNA RNA, Gene Expression, Ontologies, Proteins
2016-06-14
BioSamples Database RDF: webinar
BioSamples Database RDF: webinar from http://www.ebi.ac.uk/training/online/course/biosamples-database-rdf-webinar.
Keywords: DNA RNA, Gene Expression, Ontologies, Proteins
BioSamples Database RDF: webinar
http://www.ebi.ac.uk/training/online/course/biosamples-database-rdf-webinar
http://tess.elixir-uk.org/materials/biosamples-database-rdf-webinar
BioSamples Database RDF: webinar from http://www.ebi.ac.uk/training/online/course/biosamples-database-rdf-webinar.
DNA RNA, Gene Expression, Ontologies, Proteins
2016-06-14
ArrayExpress: Quick tour
This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress.
This course was updated in December 2015.
An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI...
Scientific topics: Gene expression, Gene expression and microarray, Functional genomics
Keywords: Gene Expression
ArrayExpress: Quick tour
http://www.ebi.ac.uk/training/online/course/arrayexpress-quick-tour-1
http://tess.elixir-uk.org/materials/arrayexpress-quick-tour
This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress.
This course was updated in December 2015.
An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI resources before taking this course.
Melissa Burke
Gene expression
Gene expression and microarray
Functional genomics
Gene Expression
Beginners
2016-06-14
