Tutorial:High Throughput Sequence Analysis With R And Bioconductor

Question

[Istvan Albert]

Visit the HT Sequence Analysis with R and Bioconductor

Synopsis: High throughput sequencing (HT-Seq or HTS), also known as next generation sequencing (NGS), presents a wide spectrum of opportunities for genome research. Unfortunately, many existing bioinformatic tools do not scale well to large datasets consisting of tens of millions of sequences generated by technologies like Illumina/Solexa, Roche/454, ABI/SOLiD and Helicos. The Bioconductor project fills this gap by providing a rapidly growing suite of well designed R packages for analyzing traditional and HT-Seq datasets. These 'BioC-Seq' packages allow to analyze these sequences with impressive speed performance. Their accelerations are achieved by using memory efficient string containers and performing the time consuming computations with calls to external programs that are implemented in compiled languages (e.g. C/C++). Together these packages form a novel framework that allows researchers to develop efficient pipelines by performing complex data analysis in a high level data analysis and programming environment.

[Vikas Bansal]

Hi, Can you please check the link. It says "Page not found".

[Vikas Bansal]

Aaah! Got it. "q" was missing at the end of the link.

Answer 1

[Leonor Palmeira]

And I would add the functionalities of seqinR (I am one of the developers but it still is a great tool :-)) :

1. to query major databases from within R
2. to manipulate fasta files and alignments files
3. to compute all sorts of statistics on sequences

See here for the manual (which I also find quite entertaining for a software manual!).