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12 materials found

Scientific topics: Sample collections  or RNA-Seq 


Tutorial on CARNIVAL

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL

Scientific topics: RNA-Seq, Omics, Gene expression, Molecular interactions, pathways and networks

Operations: RNA-Seq analysis, Network analysis

Keywords: HPC, Signaling, RNAseq, transcriptomics

Resource type: Tutorial

A Tidy Transcriptomics introduction to RNA-Seq analyses

This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.

Scientific topics: RNA-Seq

Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics

Resource type: Tutorial

Detecting differentially expressed genes with RNA-seq 11.9.2019

This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. While this course focuses on differential gene expression analysis...

Scientific topics: RNA-Seq

Bioinformatics Summer School 2019

This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are...

Scientific topics: Statistics and probability, Omics, RNA-Seq, Proteomics

Operations: Data handling

Single cell RNA-seq data analysis with R

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

RNA-Seq Lab: Workflow -- gene-level exploratory analysis and differential expression

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
Bioconductor uses the R statistical programming language, and is open source and open development.
It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Single cell RNA-seq data analysis with R

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

Single cell RNA-seq data analysis with Chipster

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

Virus detection using small RNA-seq

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

RNA-seq data analysis

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

RNA-Seq Analysis

This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of RNA-Seq data. The course starts with a comprehensive lecture covering the theory of RNA-Seq data generation and...

Scientific topics: RNA-Seq

Sample prep for Proteomics

Sample prep for proteomics by Monica Schenone.

Scientific topics: Proteomics, Sample collections