Resource type: course materials
This course covered the generation and application of large-scale holo-omic data sets, such as those produced within the HoloFood project. This course was run in September 2022, in-person in Bilbao, as part of the 1st Applied Hologenomics Conference. These course notes include the lecture slides...
Scientific topics: Metagenomics, Metabolomics, Sample collections, Metatranscriptomics
Keywords: hologenomics, metagenomics, Metabolomics, MGnify, Workshop
Resource type: Slides, course materials, hands-on tutorial
This is an international course hosted by the National Bioinformatics Infrastructure Sweden (ELIXIR-SE) in collaboration with the Human Developmental Cell Atlas (HDCA), the Royal Institute of Technology, Stockholm University, Karolinska Institutet, Uppsala University, Charité Clinical University...
Keywords: spatial, Multiomics, In situ sequencing, Spatial Transcriptomics, Single cell RNAseq
Resource type: FREE online course, course materials, online course
workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...
Scientific topics: Workflows
Keywords: Nextflow, DSL2
Resource type: Presentation, course materials
Through the Open Academy, EURORDIS empowers patient advocates to have the confidence and knowledge needed to bring their expertise to discussions on health care, research and medicines development. EURORDIS alumni engage in these discussions as equal partners, side by side with policy makers,...
Scientific topics: Rare diseases
Keywords: Rare Diseases & Research, Rare Diseases
Resource type: course materials, e-learning
"Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences.
Under this program, we have organized an intro-level workshop on data management plans, the material for which is available.
We are also organizing an advanced...
Scientific topics: Data management
Keywords: Data managment plan
Resource type: course materials
Module also available as self-study material in data carpentry style
Scientific topics: Data management
Keywords: system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers
Resource type: course materials
Programme
Monday 27.5.2019
Introduction to single cell RNA-seq (Jules Gilet)
Quality control and data preprocessing (Åsa Björklund)
Normalisation (Heli Pessa)
Removal of confounding factors (Bishwa Ghimire)
Data integration (CCA, MNN, dataset alignment) (Ahmed Mahfouz)
Tuesday...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials
This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object...
Keywords: Cloud computing, Containers
Resource type: Slides, course materials
The four day course provides a complete introduction to data science in R with the tidyverse. The course will not go deep into statistics but rather getting data ready, some exploratory analysis, visualization and handling models.
Preparing data takes up to 90% of the time spent in analysis...
Keywords: R-programming
Resource type: course materials
We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the...
Scientific topics: Protein structure analysis, Molecular biology, Evolutionary biology, Bioinformatics
Resource type: course materials
Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic
Scientific topics: Proteomics
Keywords: Galaxy, training, proteomics, eLearning, EeLP
Resource type: course materials, Training materials, Slides
Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017
Scientific topics: Microarray experiment
Keywords: life sciences, microarrays, eLearning, EeLP
Resource type: course materials, Training materials, Slides
Materials from the asynchronous learning course "ELIXIR eLearning definitions"
Keywords: eLearning, training, EeLP
Resource type: course materials, Training materials, Documentation
Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017
Scientific topics: Transcriptomics, Genomics
Keywords: transcriptomics, RNA-Seq, eLearning, EeLP
Resource type: course materials, Training materials, Slides, Video
Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
Scientific topics: Genomics
Keywords: Galaxy, training, Genomics, eLearning, EeLP
Resource type: course materials, Training materials, Slides
Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway
Scientific topics: Marine biology, Metagenomics, Genomics
Keywords: Marine Metagenomics, eLearning, EeLP
Resource type: course materials, Training materials, Slides
These are the materials of the talks and demo that were presented at the ECCB18 Workshop “Implementation of Data Management Plans & Data Stewardship in practice” on Sept 11, 2018 in Athens.
Collecting, curating, storing and exchange or sharing research data is a constant challenge that has...
Scientific topics: Data submission, annotation, and curation, Data management
Keywords: data management, data stewardship, eLearning, EeLP
Resource type: course materials, Training materials, Slides
This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials
This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials, Video
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data...
Keywords: Data analysis, Data carpentry, SoftwareCarpentry
Resource type: course materials
This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R...
Keywords: R-programming
Resource type: course materials
Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following:
- Background and motivation
- What is Git? What is version control? What is GitHub?
- How can Git and GitHub be useful for you? -...
Keywords: Git, GitHub
Resource type: course materials
This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...
Resource type: course materials, Video
This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....
Scientific topics: RNA-Seq
Resource type: course materials, Video
This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...
Scientific topics: RNA-Seq
Resource type: course materials, Video
Metagenomics investigates the composition and function of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances in high-throughput sequencing technologies, and the increasing data sizes require efficient analysis...
Scientific topics: Metagenomics
Resource type: Video, course materials