Posts Tagged ‘ Bioinformatics ’

Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE, and Pathview

December 4, 2015
By

BackgroundThis tutorial shows an example of RNA-seq data analysis with DESeq2, followed by KEGG pathway analysis using GAGE. Using data from GSE37704, with processed data available on Figshare DOI: 10.6084/m9.figshare.1601975. This dataset has six samp...

Read more »

Annotables: R data package for annotating/converting Gene IDs

November 13, 2015
By

I work with gene lists on a nearly daily basis. Lists of genes near ChIP-seq peaks, lists of genes closest to a GWAS hit, lists of differentially expressed genes or transcripts from an RNA-seq experiment, lists of genes involved in certain pathways, et...

Read more »

Software from CSHL Genome Informatics 2015

November 2, 2015
By
Software from CSHL Genome Informatics 2015

I just returned from the Genome Informatics meeting at Cold Spring Harbor. This was, hands down, the best scientific conference I've been to in years. The quality of the talks and posters was excellent, and it was great meeting in person many...

Read more »

abcfr 0.9-3

August 26, 2015
By
abcfr 0.9-3

In conjunction with our reliable ABC model choice via random forest paper, about to be resubmitted to Bioinformatics, we have contributed an R package called abcrf that produces a most likely model and its posterior probability out of an ABC reference table. In conjunction with the realisation that we could devise an approximation to the […]

Read more »

abcfr 0.9-3

August 26, 2015
By
abcfr 0.9-3

In conjunction with our reliable ABC model choice via random forest paper, about to be resubmitted to Bioinformatics, we have contributed an R package called abcrf that produces a most likely model and its posterior probability out of an ABC reference table. In conjunction with the realisation that we could devise an approximation to the […]

Read more »

Translational Bioinformatics Year In Review

April 10, 2015
By
Translational Bioinformatics Year In Review

Per tradition, Russ Altman gave his "Translational Bioinformatics: The Year in Review" presentation at the close of the AMIA Joint Summit on Translational Bioinformatics in San Francisco on March 26th.  This year, papers came from six key areas (a...

Read more »

Introduction to R for Life Scientists: Course Materials

July 7, 2014
By
Introduction to R for Life Scientists: Course Materials

Last week I taught a three-hour introduction to R workshop for life scientists at UVA's Health Sciences Library.I broke the workshop into three sections:In the first half hour or so I presented slides giving an overview of R and why R is so awesome. Du...

Read more »

Bedtools tutorial from 2013 CSHL course

June 24, 2014
By
Bedtools tutorial from 2013 CSHL course

A couple of months ago I posted about how to visualize exome coverage with bedtools and R. But if you're looking to get a basic handle on genome arithmetic, take a look at Aaron Quinlan's bedtools tutorials from the 2013 CSHL course. The tutorial uses ...

Read more »

An Annotated Online Bioinformatics / Computational Biology Curriculum

June 13, 2014
By
An Annotated Online Bioinformatics / Computational Biology Curriculum

Two years ago David Searls published an article in PLoS Comp Bio describing a series of online courses in bioinformatics. Yesterday, the same author published an updated version, "A New Online Computational Biology Curriculum," (PLoS Comput Biol 10(6):...

Read more »

Using Volcano Plots in R to Visualize Microarray and RNA-seq Results

May 28, 2014
By
Using Volcano Plots in R to Visualize Microarray and RNA-seq Results

I've been asked a few times how to make a so-called volcano plot from gene expression results. A volcano plot typically plots some measure of effect on the x-axis (typically the fold change) and the statistical significance on the y-axis (typically the...

Read more »


Subscribe

Email:

  Subscribe