TODAY San Diego R Users Group: Bioconductor for HT Sequence Data
Monday, November 22, 2010 6:30 PM
Title: Bioconductor Packages for Analyzing High Throughput Sequence Data
Speaker: Derren Barken
The San Diego R Users Group will be meeting on Monday, November 22th, from 6:30-8:30 PM at Sequenom.
The last few years have seen truly dramatic progress in next generation sequencing technologies such as Solexa (Illumina), SOLiD (Applied Biosystems) and 454 (Roche). The Bioconductor project, which is built on R, excels at working with data from these sources.
This talk will be geared for people new to Bioconductor. We will first describe motivating applications and, crucially, where to find documentation. Next, we will focus on a small number of key packages in detail: Biostrings, ShortRead, and the BSgenome packages. We will also survey other important packages such as SRAdb (for accessing the Sequence Read Archive at NCBI), rtracklayer (for UCSC genome browser data), biomaRt (for Ensembl and other data), and others. Finally, we will briefly demonstrate how aligned reads can be prepared (for Biostrings to load) using command line tools such as SOAP, MAQ and Bowtie.
Derren Barken is a Bioinformatics Scientist with Prometheus Laboratories. He completed his Ph.D. in Bioinformatics at UCSD in 2007; prior to graduate school, he worked as a programmer in Silicon Valley and Boston.
To attend this meeting, please RSVP to Vivian Huang at Sequenom. She can be reached at vhuang at scmmlab dot com, or you can reach her at [masked]. Please note that the doors will be locked after hours ? it may be necessary to call Vivian?s cell to be let in. Sequenom is located at 3595 John Hopkins Court. The entrance is in the back ? if you park in or near the visitor parking, you will be close.