Register training material
9 materials found

Authors: Jan Slifka  or Wendi Bacon 


Hands-on for 'Trajectory Analysis using Python (Jupyter Notebook) in Galaxy' tutorial

The questions this addresses are:
- How can I infer lineage relationships between single cells based on their RNA, without a time series?

\nThe objectives are:
- Execute multiple plotting methods designed to maintain lineage relationships between cells
- Interpret these plots

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Pre-processing of 10X Single-Cell RNA Datasets' tutorial

The questions this addresses are:
- What is 10X?
- What is STARsolo and what is Cell Ranger?
- What are BCL and MTX files?
- What is an HDF5 file, and why is it important?

The objectives are:
- Demultiplex single-cell FASTQ data from 10X Genomics
- Learn about transparent matrix formats
...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, 10x

Resource type: hands-on tutorial

Hands-on for 'Generating a single cell matrix using Alevin' tutorial

The questions this addresses are:
- I have some single cell FASTQ files I want to analyse. Where do I start?

The objectives are:
- Generate a cellxgene matrix for droplet-based single cell sequencing data
- Interpret quality control (QC) plots to make informed decisions on cell thresholds
...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, 10x, paper-replication, español, transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Filter, Plot and Explore Single-cell RNA-seq Data' tutorial

The questions this addresses are:
- Is my single cell dataset a quality dataset?
- How do I generate and annotate cell clusters?
- How do I pick thresholds and parameters in my analysis? What's a "reasonable" number, and will the world collapse if I pick the wrong one?

The objectives are:
...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, 10x, paper-replication, español, transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Bulk RNA Deconvolution with MuSiC' tutorial

The questions this addresses are:
- How do we infer cell type proportions from bulk RNA-seq data?
- How are these cell types grouped together?

The objectives are:
- Construct Bulk and scRNA Expression Set Objects
- Inspect these objects for various properties
- Measure the abundance of...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, mouse, human, deconvolution, bulk, transcriptomics

Resource type: hands-on tutorial

Slides for 'Plates, Batches, and Barcodes' tutorial

The questions this addresses are:
- What is a batch when it comes to single cells?
- What’s the difference between a barcode and an index?
- What is batch effect and how do you prevent it?
- What is a lane?

The objectives are:
- How to set up plates to prevent batch effect
- Proper...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell

Resource type: slides

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