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Keywords: RNA-seq  or Teaching 


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

A Tidy Transcriptomics introduction to RNA-Seq analyses https://tess.elixir-europe.org/materials/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. RNA-Seq Differential Expression, Gene Expression, RNA-seq, Transcriptomics Biologists
RNA - Seq de novo

Practical session on transciptome de novo assembly

Keywords: RNA-seq

RNA - Seq de novo https://tess.elixir-europe.org/materials/rna-seq-de-novo Practical session on transciptome de novo assembly RNA-seq
Differential analysis of RNA-Seq data

Design, describe, explore and model

Keywords: Genomics, RNA-seq

Differential analysis of RNA-Seq data https://tess.elixir-europe.org/materials/differential-analysis-of-rna-seq-data Design, describe, explore and model Genomics, RNA-seq
RNA-Seq: Differential Expression Analysis

Be careful about experimental design : avoid putting all the replicates in the same lane, using the same barcode for the replicates, putting different number of samples in lanes etc... Non- uniformity of the per base read distribution (Illumina Random Hexamer Priming bias visible on the 13...

Keywords: Differential Expression, RNA-seq, transcriptomics

RNA-Seq: Differential Expression Analysis https://tess.elixir-europe.org/materials/rna-seq-differential-expression-analysis Be careful about experimental design : avoid putting all the replicates in the same lane, using the same barcode for the replicates, putting different number of samples in lanes etc... Non- uniformity of the per base read distribution (Illumina Random Hexamer Priming bias visible on the 13 first bases) Bias hierarchy : biological condition concentration run/flowcell lane At equivalent expression level, a long gene will have more reads than a short one. Non random coverage along the transcript. Multiple hit for some reads alignments. Differential Expression, RNA-seq, transcriptomics
Eukaryotic small RNA

Small RNAseq data analysis for miRNA identification

Keywords: RNA-seq

Eukaryotic small RNA https://tess.elixir-europe.org/materials/eukaryotic-small-rna Small RNAseq data analysis for miRNA identification RNA-seq
RNA-Seq: isoform detection and quantification

transcriptome from new condition tissue-speci c transcriptome different development stages transcriptome from non model organism cancer cell RNA maturation mutant How to manage RNA-Seq data with genes subjected to di erential splicing? Is it possible to discover new isoforms? Is it...

Keywords: Isoforms, RNA-seq, Transcriptomics

RNA-Seq: isoform detection and quantification https://tess.elixir-europe.org/materials/rna-seq-isoform-detection-and-quantification transcriptome from new condition tissue-speci c transcriptome different development stages transcriptome from non model organism cancer cell RNA maturation mutant How to manage RNA-Seq data with genes subjected to di erential splicing? Is it possible to discover new isoforms? Is it possible to quantify abundance of each isoform Isoforms, RNA-seq, Transcriptomics
NGS data exploration with the MicroScope Platform

Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools

Keywords: Genomics, NGS, RNA-seq, SNP, Transcriptomics

NGS data exploration with the MicroScope Platform https://tess.elixir-europe.org/materials/ngs-data-exploration-with-the-microscope-platform Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools Genomics, NGS, RNA-seq, SNP, Transcriptomics
Differential gene expression analysis : Practical part

RNA-seq: Differential gene expression analysis practical session

Keywords: Genomics, RNA-seq

Differential gene expression analysis : Practical part https://tess.elixir-europe.org/materials/differential-gene-expression-analysis-practical-part RNA-seq: Differential gene expression analysis practical session Genomics, RNA-seq
RNA-seq: Differential gene expression analysis

Transcriptome analysis provides information about the identity and quantity of all RNA molecules

Keywords: Genomics, RNA-seq

RNA-seq: Differential gene expression analysis https://tess.elixir-europe.org/materials/rna-seq-differential-gene-expression-analysis Transcriptome analysis provides information about the identity and quantity of all RNA molecules Genomics, RNA-seq
Isoform discovery and quanti cation from RNA-Seq data

Not available

Keywords: RNA-seq

Isoform discovery and quanti cation from RNA-Seq data https://tess.elixir-europe.org/materials/isoform-discovery-and-quanti-cation-from-rna-seq-data Not available RNA-seq
The Unix Shell

The Unix Shell from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/02-shell.md.

Keywords: Teaching

The Unix Shell https://tess.elixir-europe.org/materials/the-unix-shell The Unix Shell from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/02-shell.md. Teaching Novice
Version Control with Git

Version Control with Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/03-git.md.

Keywords: Teaching

Version Control with Git https://tess.elixir-europe.org/materials/version-control-with-git Version Control with Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/03-git.md. Teaching Novice
Using Databases and SQL

Using Databases and SQL from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/05-sql.md.

Keywords: Teaching

Using Databases and SQL https://tess.elixir-europe.org/materials/using-databases-and-sql Using Databases and SQL from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/05-sql.md. Teaching Novice
Programming with Python

Programming with Python from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/04-python.md.

Keywords: Teaching

Programming with Python https://tess.elixir-europe.org/materials/programming-with-python Programming with Python from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/04-python.md. Teaching Novice
General Advice

General Advice from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/01-general.md.

Keywords: Teaching

General Advice https://tess.elixir-europe.org/materials/general-advice General Advice from https://github.com/swcarpentry/bc/tree/gh-pages/novice/teaching/01-general.md. Teaching Novice