Oqtans statistics

Citations per year

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Associated diseases

Popular tool citations

Read alignment Normalization Differential expression De novo transcriptome assembly Bioinformatics workflows Novel transcript quantification Reference-based transcriptome assembly Spliced read alignment

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Oqtans specifications

Desktop

Information

Unique identifier	OMICS_01407
Name	Oqtans
Alternative name	Online quantitative transcriptome analysis
Software type	Pipeline/Workflow
Interface	Command line interface
Restrictions to use	None
Biological technology	Illumina
Operating system	Unix/Linux, Mac OS
Programming languages	C, C++, Java, MATLAB, Perl, Python, R
License	GNU General Public License version 2.0
Computer skills	Advanced
Stability	Stable
Maintained	Yes

Versioning

No version available

Maintainers

Gunr Rätsch
Vipin Sreedharan

Publication for Online quantitative transcriptome analysis

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

2014 Bioinformatics

PMCID: 3998122

PMID: 24413671

DOI: 10.1093/bioinformatics/btt731

Oqtans citations

(2)

Scalability and Validation of Big Data Bioinformatics Software

2017

Comput Struct Biotechnol J

PMCID: 5537105

PMID: 28794828

DOI: 10.1016/j.csbj.2017.07.002

[…] s. There have been many bioinformatics SaaS solutions to perform tasks ranging from short-read alignment (CloudAligner and SparkBWA ), variant calling (Halvade and Churchill ) and RNA-seq analysis (Oqtans and Falco ). In Platform as a Service, users are provided with a platform for developing their own software. Some PaaS providers also provide support for automatically scaling the computing re […]

Highlights from the ISCB Student Council Symposium 2013

2014

BMC Bioinformatics

PMCID: 4079984

PMID: 25077567

DOI: 10.1186/1471-2105-15-S3-A1

[…] replicate previous tuberculosis loci, and to introduce novel genes and sub-networks underlying ethnic differences in tuberculosis risk.In the last oral presentation, Sreedharan et al. [12] presented Oqtans: A MultifunctionalWorkbench for RNAseq Data Analysis. To assist the investigation of the abundance of RNA transcripts and their potential differential expression, the workbench enables research […]

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Oqtans institution(s)

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Machine Learning in Biology Group, Friedrich Miescher Laboratory, Tübingen, Germany; LINA, Combinatorics and Bioinformatics Group, University of Nantes, Nantes, France; Machine Learning/Intelligent Data Analysis Group, Technical University, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

Oqtans funding source(s)

Supported by Max Planck Society, the German Research Foundation (RA1894/1-1 and RA1894/2-1) and the Memorial SloanKettering Cancer Center (MSKCC).

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