VERSE v1.0.5 – Versatile and Efficient RNA-Seq Read Counting Tool

VERSE v1.0.5

:: DESCRIPTION

VERSE is designed for high-performance read summarization for next generation sequencing. VERSE is 50x faster than HTSeq when computing the same gene counts. It introduces a novel, hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. There is also a set of parameters the user can use to fine-tune the assignment logic. VERSE can be readily incorporated into any existing RNA-Seq analysis pipelines.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

VERSE 

:: MORE INFORMATION

Citation

Zhu, Q., Fisher, S.A., Shallcross, J., Kim, J. (Preprint).
VERSE: a versatile and efficient RNA-Seq read counting tool. bioRxiv 053306.
doi: http://dx.doi.org/10.1101/053306

FlyNet – Versatile Network Prioritization server for Drosophila Melanogaster

FlyNet

:: DESCRIPTION

FlyNet is a network prioritization server for the Drosophila melanogaster biology. The FlyNet web server is specialized for the generation of versatile hypothesis in Drosophila-based studies.

::DEVELOPER

NetBioLab, Yonsei University, Seoul, Korea.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FlyNet: a versatile network prioritization server for the Drosophila community.
Shin J, Yang S, Kim E, Kim CY, Shim H, Cho A, Kim H, Hwang S, Shim JE, Lee I.
Nucleic Acids Res. 2015 Jul 1;43(W1):W91-7. doi: 10.1093/nar/gkv453.

IgSimulator – Versatile tool for Simulation of Immunoglobulin Repertoire

IgSimulator

:: DESCRIPTION

IgSimulator is a tool for simulation of antibody repertoire and Ig-seq library. IgSimulator is designed for testing and benchmarking tools for reconstruction of Ig repertoires.

::DEVELOPER

Yana Safonova (Center for Algorithmic Biotechnology, Saint Petersburg State University).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 IgSimulator

:: MORE INFORMATION

Citation

IgSimulator: a versatile immunosequencing simulator.
Safonova Y, Lapidus A, Lill J.
Bioinformatics. 2015 May 25. pii: btv326.

VEGAS 0.8.27 – Versatile Gene-based Association Study

VEGAS 0.8.27

:: DESCRIPTION

VEGAS (Versatile Gene-based Association Study) is a free program for performing gene-based tests for association using the results from genetic association studies. After reading in SNP association p-values, it will annotate SNPs according to their position in genes, produce a gene-based test statistic, and then use simulation to calculate an empirical gene-based p-value.

::DEVELOPER

Jimmy Liu  and Stuart MacGregor

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 VEGAS

:: MORE INFORMATION

Citation

Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM, AMFS Investigators, Hayward NK, Montgomery GW, Visscher PM, Martin NG, MacGregor S. (2010).
A Versatile Gene-Based Test for Genome-wide Association Studies.
American Journal of Human Genetics, 87.

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