ade4 1.7-13 / ade4TkGUI 0.2-9 – Ecological Data Analysis

ade4 1.7-13 / ade4TkGUI 0.2-9

:: DESCRIPTION

The ade4 package (Data Analysis functions to analyze Ecological and Environmental data in the framework of Euclidean Exploratory methods) is a complete rewrite for the R environment  of the ADE-4 (in uppercase) software.The ade4 package for the R statistical environment proposes a great number of multivariate methods. Its implementation follows the tradition of the French school of ”Analyse des Donn′ees” and is based on the use of the duality diagram.

ade4TkGUI is an R package providing a graphical user interface for some basic functions of the multivariate data analysis package ade4.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ade4 ; ade4TkGUI

:: MORE INFORMATION

References :

BURRITO – Visualization Tool for Exploratory Data Analysis of Metagenomic data

BURRITO

:: DESCRIPTION

BURRITO is a web-based tool for interactive exploration of metagenomic datasets, linking taxonomic and functional microbiome profiles

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

BURRITO

:: MORE INFORMATION

Citation

Front Microbiol. 2018 Mar 1;9:365. doi: 10.3389/fmicb.2018.00365. eCollection 2018.
BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data.
McNally CP, Eng A, Noecker C, Gagne-Maynard WC, Borenstein E.

expVIP 20180914 – RNA-seq Data Analysis and Visualization Platform

expVIP 20180914

:: DESCRIPTION

ExpVIP (expression visualization and integration platfor) is a tool that enables the integration of different RNA-Seq studies by analysing the data uniformly across experiments and provides a web interface to query the data.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

expVIP

:: MORE INFORMATION

Citation

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.
Borrill P, Ramirez-Gonzalez R, Uauy C.
Plant Physiol. 2016 Apr;170(4):2172-86. doi: 10.1104/pp.15.01667.

Philosopher 2.0.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 2.0.0

:: DESCRIPTION

Philosopher provides easy access to third-party tools and custom algorithms for proteomics analysis, from database searching to functional protein reports. Philosopher is also well-equipped for open search analysis, providing extended versions of PeptideProphet and ProteinProphet for peptide validation and protein inference.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Philosopher

:: MORE INFORMATION

MetaR 2.0.2 – Data Analysis with the R Ecosystem

MetaR 2.0.2

:: DESCRIPTION

MetaR (Metaprogramming in R) takes advantage of Language Workbench Technology to facilitate data analysis with the R language.

::DEVELOPER

Campagne Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

MetaR

:: MORE INFORMATION

Citation

Fabien Campagne, William ER Digan, Manuele Simi
MetaR: simple, high-level languages for data analysis with the R ecosystem
bioRxiv 2015 doi: http://dx.doi.org/10.1101/030254

PopGenome 2.7.1 – Data Analysis in Population Genetics

PopGenome 2.7.1

:: DESCRIPTION

The PopGenome library provides data analysis in population genetics and is programmed in the powerful, open-source, statistical computing environment R. Several polymorphism statistics, such as the number of segregating sites and nucleotide or haplotype diversity based FST measurements can be calculated. In addition, PopGenome contributes a lot of neutrality statistics such as the Tajima D and Rozas R2 test. Testing of the significance of these statistics requires generating bootstrap samples from a neutral model using a coalescent approach.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PopGenome

:: MORE INFORMATION

Citation:

Mol Biol Evol. 2014 Jul;31(7):1929-36. doi: 10.1093/molbev/msu136. Epub 2014 Apr 16.
PopGenome: an efficient Swiss army knife for population genomic analyses in R.
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ

Mayday 2.14 – Microarray Data Analysis

Mayday 2.14

:: DESCRIPTION

Mayday (Microarray Data Analysis)is a workbench for visualization, analysis and storage of microarray data.

Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods.

In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources. This meta information can be used to enhance visualizations, such as in the enhanced heatmap visualization.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Mayday

:: MORE INFORMATION

Citation

Florian Battke, Stephan Symons and Kay Nieselt: Mayday – Integrative analytics for expression data;
BMC Bioinformatics 11 (1):121 (2010)

Perseus 1.5.2.6 – Shotgun Proteomics Data Analysis

Perseus 1.5.2.6

:: DESCRIPTION

is a software package for shotgun proteomics data analysis, which helps researchers to extract biologically meaningful information from their MaxQuant output such as posttranslational modifications.

::DEVELOPER

Jürgen Cox

:: SCREENSHOTS

Perseus

:: REQUIREMENTS

  • Windows 64bit
  • .NET Framework 4.5

:: DOWNLOAD

 Perseus

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 16:S12. doi: 10.1186/1471-2105-13-S16-S12. Epub 2012 Nov 5.
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.
Cox J, Mann M.

ARB 6.0.3 – Sequence Database Handling and data analysis

ARB 6.0.3

:: DESCRIPTION

The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.

::DEVELOPER

Lehrstuhl für Mikrobiologie, TU München

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ARB

:: MORE INFORMATION

Citation:

Wolfgang Ludwig, et al.
ARB: a software environment for sequence data.
Nucleic Acids Research. 2004. 32(4):1363-1371.

ProteoWizard 3.0.9134 – Proteomics Data Analysis

ProteoWizard 3.0.9134

:: DESCRIPTION

ProteoWizard is a modular and extensible set of open-source, cross-platform tools and software libraries for proteomics data analysis.The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

::DEVELOPER

ProteoWizard Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

ProteoWizard

:: MORE INFORMATION

Citation

Kessner D, Chambers M, Burke R, Agus D, Mallick P.
ProteoWizard: open source software for rapid proteomics tools development.
Bioinformatics. 2008 Nov 1;24(21):2534-6. Epub 2008 Jul 7.