Bérénice Batut
Favourite Topics
Favourite Formats
Contributions
The following list includes only slides and tutorials where the individual has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.
GitHub Activity
Tutorials
- Epigenetics / Identification of the binding sites of the Estrogen receptor
- Epigenetics / Formation of the Super-Structures on the Inactive X
- Statistics and machine learning / Machine learning: classification and regression
- Teaching and Hosting Galaxy training / Running a workshop as instructor
- Teaching and Hosting Galaxy training / Set up a Galaxy for Training
- Teaching and Hosting Galaxy training / Organizing a workshop
- Foundations of Data Science / Advanced R in Galaxy
- Foundations of Data Science / R basics in Galaxy
- Using Galaxy and Managing your Data / RStudio in Galaxy
- Sequence analysis / Mapping
- Sequence analysis / Quality Control
- Development in Galaxy / Data source integration
- Genome Annotation / Essential genes detection with Transposon insertion sequencing
- Contributing to the Galaxy Training Material / Including a new topic
- Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours
- Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials
- Contributing to the Galaxy Training Material / Running the GTN website locally
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line
- Contributing to the Galaxy Training Material / Creating content in Markdown
- Contributing to the Galaxy Training Material / Creating a new tutorial
- Contributing to the Galaxy Training Material / Contributing with GitHub via its interface
- Contributing to the Galaxy Training Material / Generating PDF artefacts of the website
- Metagenomics / Metatranscriptomics analysis using microbiome RNA-seq data (short)
- Metagenomics / 16S Microbial Analysis with mothur (short)
- Metagenomics / Analyses of metagenomics data - The global picture
- Metagenomics / 16S Microbial Analysis with mothur (extended)
- Metagenomics / Metatranscriptomics analysis using microbiome RNA-seq data
- Ecology / Regional GAM
- Ecology / Species distribution modeling
- Transcriptomics / Reference-based RNA-Seq data analysis
- Transcriptomics / Pre-processing of Single-Cell RNA Data
- Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
- Transcriptomics / Clustering 3K PBMCs with Scanpy
- Transcriptomics / RNA Seq Counts to Viz in R
- Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease
- Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
- Introduction to Galaxy Analyses / From peaks to genes
Slides
- Epigenetics / Introduction to ChIP-Seq data analysis
- Development in Galaxy / Galaxy from a developer point of view
- Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material
- Metagenomics / Introduction to metagenomics
- Transcriptomics / Introduction to Transcriptomics
- Variant Analysis / Introduction to Variant analysis
- Introduction to Galaxy Analyses / Introduction to Galaxy
- Epigenetics / ChIP-seq data analysis
- Galaxy Server administration / Docker and Galaxy
- Sequence analysis / Quality Control
- Development in Galaxy / Tool development and integration into Galaxy
- Development in Galaxy / Tool Shed: sharing Galaxy tools
- Development in Galaxy / Galaxy Interactive Tours
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line
- Contributing to the Galaxy Training Material / Creating Slides
News
Saskia Hiltemann
Helena Rasche
Bérénice Batut
Anthony Bretaudeau
Yvan Le Bras
Fotis E. Psomopoulos
The Carpentries
Erasmus+ Programme
As part of our work under the Gallantries Grant we are establishing a new topic within the GTN specifically focused on Data Science skills. This topic will include tutorials covering things such as:
Full Story
Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.
Full Story
As you have probably already seen, a feedback form is embedded on the bottom of each tutorial.
Full Story
Wolfgang MaierEffectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.
Full Story
Snippets have received an major overhaul! Snippets/FAQs are small reusable bits of training, often answering a single question. In addition to the general Galaxy snippets, we now also support topic-level and tutorial-level FAQs. This will allow contributors to add common questions and answers to their tutorials, which not only can be included in the tutorial text itself, but are also used to autogenerate an FAQ page for the tutorial or topic listing all common questions (and answers).This will be useful both to participants following tutorials via self-study, and also to instructors preparing for a training event.
Full Story
Saskia Hiltemann
Helena Rasche
Bérénice Batut
Jennifer Hillman-Jackson
Delphine Lariviere
Anna Syme
Maria Doyle
Every 3 months we organise one day dedicated to the GTN community! Thursday, May 20th is the next GTN CoFest. We will be working on the training materials, have discussions with the global Galaxy traning community. Do you teach with Galaxy? Want to learn how to add your tutorial to the GTN? New to the community and just want to learn more? Everybody is welcome!
Full Story