Tutorial: High Throughput Sequence Analysis With R And Bioconductor
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gravatar for Istvan Albert
8.2 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

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.

bioconductor tutorial • 4.7k views
ADD COMMENTlink modified 8.2 years ago by Leonor Palmeira3.7k • written 8.2 years ago by Istvan Albert ♦♦ 85k

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

ADD REPLYlink written 8.2 years ago by Vikas Bansal2.4k

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

ADD REPLYlink written 8.2 years ago by Vikas Bansal2.4k
4
gravatar for Leonor Palmeira
8.2 years ago by
Leonor Palmeira3.7k
Liège, Belgium
Leonor Palmeira3.7k wrote:

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!).

ADD COMMENTlink written 8.2 years ago by Leonor Palmeira3.7k
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