Register training material
8 materials found

Authors: Jan Slifka  or Pavankumar Videm 


Hands-on for 'RNA-RNA interactome data analysis' tutorial

The questions this addresses are:
- What are the difficulties in mapping chimeric reads from RNA interactome data?
- How multi mapping is a big problem in these datasets?
- How to filter for meaningful results from large analysis output files?

The objectives are:
- Quality control and data...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Whole transcriptome analysis of Arabidopsis thaliana' tutorial

The questions this addresses are:
- Which miRNAs are upregulated in response to brassinosteroids?
- Which genes are potential target of brassinosteroid-induced miRNAs?

The objectives are:
- Perform miRNA differential expression analysis
- Understand the quasi-mapping-based Salmon method...

Scientific topics: Transcriptomics

Keywords: transcriptomics, miRNA, plants, stress tolerance

Resource type: hands-on tutorial

Hands-on for 'Analysis of plant scRNA-Seq Data with Scanpy' tutorial

The questions this addresses are:
- Can we reclaim cell markers using a different analysis method?
- Are highly variable genes paramount to the analysis?

The objectives are:
- Perform filtering, dimensionality reduction, and clustering
- Generate a DotPlot emulating the original paper...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, plants, paper-replication

Resource type: hands-on tutorial

Hands-on for 'Small Non-coding RNA Clustering using BlockClust' tutorial

The questions this addresses are:
- What do the read profiles of small non-coding RNAs represent?
- How to cluster the read profiles based on some intrinsic features?

The objectives are:
- Difference between mRNA-seq and smallRNA-seq
- Unsupervised grouping of the adjacent reads into read...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Reference-based RNA-Seq data analysis' tutorial

The questions this addresses are:
- What are the steps to process RNA-Seq data?
- How to identify differentially expressed genes across multiple experimental conditions?
- What are the biological functions impacted by the differential expression of genes?

The objectives are:
- Check a...

Scientific topics: Transcriptomics

Keywords: transcriptomics, bulk, rna-seq, collections, drosophila, QC, cyoa

Resource type: hands-on tutorial

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides