BAMTOOLS 2.5.1 – C++ API and Toolkit for Analyzing and Managing BAM files

BAMTOOLS 2.5.1

:: DESCRIPTION

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BAMTOOLS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1691-2. Epub 2011 Apr 14.
BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Barnett DW, Garrison EK, Quinlan AR, , Strömberg MP, Marth GT.

Comb-p 0.43 – Combining, Analyzing, Grouping and Correcting Spatially Correlated P-values

Comb-p 0.43

:: DESCRIPTION

comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions.

::DEVELOPER

Katerina Kechris , Brent Pedersen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 Comb-p

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ.

MetaOmGraph 1.4.1 – Plotting and Analyzing large sets of Biological data

MetaOmGraph 1.4.1

:: DESCRIPTION

MetaOmGraph is a tool for plotting and analyzing large sets of data while using as little memory as possible. It was designed with biological experiment data in mind.

::DEVELOPER

MetNet Workshops

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 MetaOmGraph

:: MORE INFORMATION

Citation:

Chem Biodivers. 2012 May;9(5):868-87. doi: 10.1002/cbdv.201100355.
Massive human co-expression network and its medical applications.
Feng Y, Hurst J, Almeida-De-Macedo M, Chen X, Li L, Ransom N, Wurtele ES.

GenomicTools 2.8.0 – Flexible Computational Platform for Analyzing Genomic data

GenomicTools 2.8.0

:: DESCRIPTION

GenomicTools is a flexible open-source computational platform for the analysis, manipulation and visualization of high-throughput sequencing data.

::DEVELOPER

Dr. Tsirigos

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GenomicTools

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 15;28(2):282-3. doi: 10.1093/bioinformatics/btr646. Epub 2011 Nov 22.
GenomicTools: a computational platform for developing high-throughput analytics in genomics.
Tsirigos A1, Haiminen N, Bilal E, Utro F.

AcE 0.5 – A System for Analyzing the Accuracy of Gene Prediction Programs

AcE 0.5

:: DESCRIPTION

AcE is a program to aid gene prediction accuracy evaluation. It uses GFF format to make it easy to convert gene prediction results into an analyzable format. Novel features include isoform accuracy evaluation from either the annotated gene or gene prediction perspective or both at the same time. Masking of genomic sequence which has unknown features allows gene predictions in annotated regions to be analyzed in a genomic context. Test sets, such as an artificial sequence test set or genomic context test set, can be generated by selecting specified annotated sequences from a master set.

::DEVELOPER

William.S.Hayes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Perl

:: DOWNLOAD

   AcE

:: MORE INFORMATION

JSim 2.15 – Simulation System for Building and Analyzing Quantitative Numeric Models

JSim 2.15

:: DESCRIPTION

JSim is a Java-based simulation system for building and analyzing quantitative numeric models. JSim’s primary focus has been in physiology and bio-medicine, however its computation engine is quite general and applicable to a wide range of scientific domains.

::DEVELOPER

Erik Butterworth

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 JSim

:: MORE INFORMATION

Citation

JSim, an open-source modeling system for data analysis.
Butterworth E, Jardine BE, Raymond GM, Neal ML, Bassingthwaighte JB.
F1000Res. 2013 Dec 30;2:288. doi: 10.12688/f1000research.2-288.v1.

metano 1.0 – Analyzing the Capabilities of Metabolic Networks

metano 1.0

:: DESCRIPTION

metano is an open-source software toolbox for analyzing the capabilities of metabolic networks and for assisting in metabolic reconstruction.

::DEVELOPER

Alexander Riemer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Python

:: DOWNLOAD

 metano

:: MORE INFORMATION

Citation

Riemer SA, Rex R, Schomburg D.
A metabolite-centric view on flux distributions in genome-scale metabolic models.
BMC Syst Biol, 7:33 (2013).

MetATT – Metabolomics tool for Analyzing Two-factor and Time-series data

MetATT

:: DESCRIPTION

MetATT is a easy-to-use, web-based tool designed for time-series and two-factor metabolomics data analysis. MetATT offers a number of complementary approaches including 3D interactive principal component analysis, two-way heatmap visualization, two-way ANOVA, ANOVA-simultaneous component analysis and multivariate empirical Bayes time-series analysis.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • R package
  • Apache Tomcat 6.0 or Glassfish v2/v3.

:: DOWNLOAD

  MetATT

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2455-6. doi: 10.1093/bioinformatics/btr392. Epub 2011 Jun 27.
MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets.
Xia J, Sinelnikov IV, Wishart DS.

nucloc 1.06 – Analyzing Gene Positions in the Yeast Nucleus

nucloc 1.06

:: DESCRIPTION

nucloc is a set of computational tools designed to analyze gene positioning in yeast nuclei by automated processing of fluorescence microscopy images.

::DEVELOPER

Computational Imaging & Modeling Group,  Institut Pasteur

:: SCREENSHOTS

nucloc

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Matlab

:: DOWNLOAD

 nucloc

:: MORE INFORMATION

Citation:

Nat Methods. 2008 Dec;5(12):1031-7. doi: 10.1038/nmeth.1266. Epub 2008 Nov 2.
High-resolution statistical mapping reveals gene territories in live yeast.
Berger AB, Cabal GG, Fabre E, Duong T, Buc H, Nehrbass U, Olivo-Marin JC, Gadal O, Zimmer C.

RDNAanalyzer – Secondary Structure Pprediction and Analyzing DNA

RDNAanalyzer

:: DESCRIPTION

RDNAanalyzer is a computer based tool designed for analysis of nucleotide sequences in DNA and RNA.

::DEVELOPER

Muhammad Afzal @ CEMB

:: SCREENSHOTS

RDNAanalyzer

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 RDNAanalyzer

:: MORE INFORMATION

Citation

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.
Afzal M, Shahid AA, Shehzadi A, Nadeem S, Husnain T.
Bioinformation. 2012;8(14):687-90. doi: 10.6026/97320630008687. Epub 2012 Jul 21