Register training material
3 materials found

Content provider: GOBLET 

and

Authors: Jared Simpson  or Eija Korpelainen  or Maria Victoria .  or Julie Sullivan  or Friederike Ehrhart  or nekrut  or Boris Steipe  or Pedro Fernandes 


RNA-seq data analysis: from raw reads to differentially expressed genes

This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of...

Scientific topics: Sequencing, RNA, Data architecture, analysis and design, Bioinformatics

Keywords: Bioinformatics, Differential expression, Ngs, Rna seq

RNA-seq data analysis: from raw reads to differentially expressed genes https://tess.elixir-europe.org/materials/rna-seq-data-analysis-from-raw-reads-to-differentially-expressed-genes This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of 10-30 minute lectures intertwined with hands-on exercises, and it can be accomplished in a day. As the user-friendly Chipster software is used in the exercises, no prior knowledge of R/Bioconductor or Unix ir required, and the course is thus suitable for everybody. Our book RNA-seq data analysis: A practical approach (CRC Press) can be used as background reading. The following topics and analysis tools are covered: 1. Introduction to the Chipster analysis platform 2. Quality control of raw reads (FastQC, PRINSEQ) 3. Preprocessing (Trimmomatic, PRINSEQ) 4. Alignment to reference genome (TopHat2) 5. Alignment level quality control (RseQC) 6. Quantitation (HTSeq) 7. Experiment level quality control with PCA and MDS plots 8. Differential expression analysis (DESeq2, edgeR) -normalization -dispersion estimation -statistical testing -controlling for batch effects, multifactor designs -filtering -multiple testing correction 9. Visualization of reads and results -genome browser -Venn diagram -volcano plot -plotting normalized counts for a gene -expression profiles 10. Experimental design Sequencing RNA Data architecture, analysis and design Bioinformatics Bioinformatics, Differential expression, Ngs, Rna seq Bench biologists Life Science Researchers 2015-12-04 2017-10-09
A mind map is a nice visual way of describing the content of a training course

A Mind Map can be built by arranging boxes with subject titles in a variety of ways. In this example, the objective was to create a visual aid to better understand the relationship between the subjects that had been covered. The diagram is centered in the core subject, and other subjects occupy...

Keywords: Mind map, Training technique, Visual aid

A mind map is a nice visual way of describing the content of a training course https://tess.elixir-europe.org/materials/a-mind-map-is-a-nice-visual-way-of-describing-the-content-of-a-training-course A Mind Map can be built by arranging boxes with subject titles in a variety of ways. In this example, the objective was to create a visual aid to better understand the relationship between the subjects that had been covered. The diagram is centered in the core subject, and other subjects occupy successive layers showing hierarchy. This diagram was generated at the end of the GTPB training course SMLMC15 - Structural Modelling for Large Macromolecular Complexes with Joanna Kasprzak and Mateusz Dobrychłop It was prepared using the X-Mind software (free version) Mind map, Training technique, Visual aid Structural Biologists Training Designers Training instructors 2015-05-09 2017-10-09
"Key-terms", a learning game for conceptual consolidation

A short presentation describing a new participatory method that easily engages course participants in gamestorming and helps to consolidate new knowledge, by collectively agreeing on ways to place concepts in mind maps. "Key-terms" is a classroom game that can be played in a variety of contexts,...

Keywords: Education, Instruction, Training

"Key-terms", a learning game for conceptual consolidation https://tess.elixir-europe.org/materials/key-terms-a-learning-game-for-conceptual-consolidation A short presentation describing a new participatory method that easily engages course participants in gamestorming and helps to consolidate new knowledge, by collectively agreeing on ways to place concepts in mind maps. "Key-terms" is a classroom game that can be played in a variety of contexts, from group discussions to several forms of Non-Formal learning (e.g. training) events. It helps a lot in engaging a small audience, following any wrap-up (recapitulation) session. Learners capture terms that they find conceptually important and contribute to a merged list. Then they are invited to pin these terms on a cork board in specified ways, such as placing related terms together (clustering), placing high order terms above lower order ones, etc. The instructor/facilitator can intervene at several levels in minimal, non-disturbing interventions, that help to contextualise what is happening. A depiction of how concepts are perceived in a class emerges quickly. This is, in practice, a visual concept map. The technique is being tested in the context of technical training provision, with the help of IT. Education, Instruction, Training Educators Ontologists Trainers 2014-07-06 2017-10-09