Archive For June 2011

Using R: a guide for complete beginners

on June 21, 2011 by Alastair Kerr in Statistics, Tutorials, Comments (2)

This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that  biologists need to perform  some basic analysis:  load a […]

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Differential Producibility Analysis (DPA) of transcriptomic data to help understand metabolic status of a cell or microorganism

on by Bhushan Bonde in Metabolic modelling, Statistics, Systems Biology, Transcriptomics, Tutorials, Comments (2)

Bhushan Bonde Introduction While a vast amount of microarray data is now available freely at the various repositories at NCBI (GEO database) and EBI (ArrayExpress), there is currently no […]

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Accessing Ensembl using Ruby – the Core database

on by Jan Aerts in Bioinformatics APIs, Comments (2)

This tutorial describes how to use the Ruby API to the Ensembl Core database. It is part of a collection of 3 tutorials on the Ruby API to Ensembl. […]

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Kinetic modelling of metabolic pathways

on by Natalie Stanford and Kieran Smallbone in Metabolic modelling, Comments (2)

Authors Natalie J Stanford1,2 , Kieran Smallbone2,3 1. Integrative Systems Biology Doctoral Training Centre; 2. Manchester Centre for Integrative Systems Biology; and 3. School of Mathematics, University of Manchester, […]

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Volcano plots of microarray data

on by Colin Gillespie in Transcriptomics, Tutorials, Comments (9)

To run the R commands in this post, you should first work through Analysing microarry data in BioConductor. A volcano plot is a scatter plot that is often used when […]

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Desktop Sequence Analysis: software review

on by Alastair Kerr in Software Comparisons, Comments (1)

Shaun Webb, Alastair RW Kerr A brief summary of the most popular sequence analysis programs in currently in use. All of these programs are compatible with VectorNTI file types […]

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Accessing Ensembl using Ruby

on by Jan Aerts in Bioinformatics APIs, Comments (5)

This tutorial describes how to use the Ruby API to the Ensembl Core and Variation databases. It is intended as an introduction and demonstration of the general API concepts. […]

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Gene Set Enrichment Analysis

on June 20, 2011 by Simon Cockell in Transcriptomics, Comments (4)

Introduction The enrichment analysis explored in the previous article can be powerful provided the mechanism used for identifying candidate genes finds all of the genes that are interesting in […]

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Downstream functional analysis of an ‘omics experiment using freely available tools

on by Simon Cockell in Transcriptomics, Comments (4)

Introduction The direct analysis of data from ‘omics experiments (transcriptomics and proteomics especially), focusses on producing lists of genes or proteins of interest (i.e. those that vary in expression, […]

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Analysing microarray data in BioConductor: figures and code

on by Daniel Swan in Transcriptomics, Tutorials, Comments (2)

From the previous article on “Analysing microarray data in BioConductor” the complete code listing is below. Please ensure you have your phenodata.txt file in the right directory to start […]

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