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6 materials found

Authors: Mick Watson  or Charlotte Soneson 


Microbial genomics

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...

Keywords: Microbiome

Microbial genomics https://tess.elixir-europe.org/materials/microbial-genomics 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 active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Microbiome
Experimental design

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...

Keywords: Experimental design

Experimental design https://tess.elixir-europe.org/materials/experimental-design 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 active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Experimental design
New RNA-seq workflows

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...

Keywords: RNAseq

New RNA-seq workflows https://tess.elixir-europe.org/materials/new-rna-seq-workflows 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 active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. RNAseq
Working with Affymetrix CEL files in R

This tutorial shows how to download some public Affymetrix microarray data, load the data into R, calculate expression values and do some very simple plotting

Keywords: Affymetrix, Microarrays, R

Working with Affymetrix CEL files in R https://tess.elixir-europe.org/materials/working-with-affymetrix-cel-files-in-r This tutorial shows how to download some public Affymetrix microarray data, load the data into R, calculate expression values and do some very simple plotting Affymetrix, Microarrays, R Beginners PhD students Researchers 2014-01-14 2017-10-09
Simple plotting in R

This quick and simple tutorial demonstrates some of the easy plotting tools in the R core software. the data are in the "data" directory and come from an old two-colour microarray experiment where spots on the array were printed with different buffers, in different concentrations and with...

Keywords: Bioinformatics, Microarray data analysis, Plotting data, R, Visualisation

Simple plotting in R https://tess.elixir-europe.org/materials/simple-plotting-in-r This quick and simple tutorial demonstrates some of the easy plotting tools in the R core software. the data are in the "data" directory and come from an old two-colour microarray experiment where spots on the array were printed with different buffers, in different concentrations and with different pins.  Also, both channels Cy5 and Cy3 were spotted identically, and so the fold ratio for all spots should be 1 - this helps us see bias in the data Bioinformatics, Microarray data analysis, Plotting data, R, Visualisation Beginners PhD students Researchers Scientists 2014-01-14 2017-10-09
Quality Control of Illumina Sequencing data in the cloud

This course was created as part of the SeqAhead project and contains both powerpoint presentations and course materials that teach students how to set up an Amazon EC2 virtual machine, connect to it, download some Illumina data from  the short read archive (SRA), assess the quality of the data...

Keywords: Bioinformatics, Cloud, Next generation sequencing, Next generation sequencing data analysis, Ngs bioinformatics, Qc ngs data

Quality Control of Illumina Sequencing data in the cloud https://tess.elixir-europe.org/materials/quality-control-of-illumina-sequencing-data-in-the-cloud This course was created as part of the SeqAhead project and contains both powerpoint presentations and course materials that teach students how to set up an Amazon EC2 virtual machine, connect to it, download some Illumina data from  the short read archive (SRA), assess the quality of the data and learn to trim both bad quality bases and adapter sequences Bioinformatics, Cloud, Next generation sequencing, Next generation sequencing data analysis, Ngs bioinformatics, Qc ngs data Beginners 2014-01-13 2017-10-09