Tag: Data Analysis

AMEN 1.5.5 – Molecular Systems Biology Data Analysis

AMEN 1.5.5

:: DESCRIPTION

AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.

::DEVELOPER

Frédéric Chalmel and Michael Primig

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  AMEN

:: MORE INFORMATION

Citation:

Frédéric Chalmel and Michael Primig
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
BMC Bioinformatics 2008, 9:86doi:10.1186/1471-2105-9-86

CDAO 2019-06-26 – Comparative Data Analysis Ontology

CDAO 2019-06-26

:: DESCRIPTION

CDAO provides extensive conceptual coverage of commonly used concepts in evolutionary analyses in a single framework. It is developed in collaboration with a group of domain scientists specialising in phylogenetic analysis software, the EvoInfo working group (http://evoinfo.nescent.org) . CDAO is used in a number of projects, including nexML, Nexplorer3, TreeBASE, phyloXML.

::DEVELOPER

the Evolutionary Informatics working group of the National Evolutionary Synthesis Center (NESCent).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CDAO

:: MORE INFORMATION

Citation:

Evol Bioinform Online. 2009 Jul 3;5:47-66.
Initial implementation of a comparative data analysis ontology.
Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A.

QTModel 0.70Beta – Mixed Linear Model Analysis, Microarray Data Analysis and Diallele Cross Analysis

QTModel 0.70Beta

:: DESCRIPTION

QTModel is user-friendly computer software which packaged with modules for microarray data analysis, diallele design analysis and mixed model analysis.The mixed model module is developed for analyzing data from experimental designs with random factors. It is now available for commonly used randomized block design, randomized complete block design, latin square design, factorial design, multi-factor factorial design, nested design, and cross nested design etc. For fixed factors, pair-wised comparisons are done for all possible pairs of fixed effects of one factor. For random factors, some mixed linear model approaches, such as MINQUE, MIVQUE, REML and EM, will be used to estimate the variances of these random factors, and also unbiased prediction methods, such as BLUP, LUP and AUP, are used to predict the random effects of the random factors.

::DEVELOPER

ZJU-IBI

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 QTModel

:: MORE INFORMATION

Citation

Funct Integr Genomics. 2009 Feb;9(1):59-66. Epub 2008 Sep 5.
Identifying differentially expressed genes in human acute leukemia and mouse brain microarray datasets utilizing QTModel.
Yang J, Zou Y, Zhu J.

S-Mart 1.1.4 – Aid RNA-seq Data Analysis

S-Mart 1.1.4

:: DESCRIPTION

S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.

::DEVELOPER

URGI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 S-Mart

:: MORE INFORMATION

Citation

Matthias Zytnicki
S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
PLoS One. 2011; 6(10): e25988.

Philosopher 4.0.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 4.0.0

:: 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

Citation

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI.
Philosopher: a versatile toolkit for shotgun proteomics data analysis.
Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.

mzMatch/PeakML 2.0 – Metabolomics Data Analysis

mzMatch/PeakML 2.0

:: DESCRIPTION

mzMatch is a modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language. It was designed to provide small tools for the common processing tasks for LC/MS data. The mzMatch environment was based entirely on the PeakML file format and core library, which provides a common framework for all the tools.

::DEVELOPER

mzMatch team

:: SCREENSHOTS

mzMatch

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java/ R

:: DOWNLOAD

 mzMatch/PeakML

:: MORE INFORMATION

Citation

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.
Scheltema RA, Jankevics A, Jansen RC, Swertz MA, Breitling R.
Anal Chem. 2011 Apr 1;83(7):2786-93. doi: 10.1021/ac2000994

Sipros 3.0 – Proteomics Data Analysis software

Sipros 3.0

:: DESCRIPTION

Sipros is a database-searching algorithm for peptide and protein identification in shotgun proteomics.

:: DESCRIPTION

the Pan lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python
  • R package

:: DOWNLOAD

 Sipros

:: MORE INFORMATION

Citation

Sipros/ProRata: a versatile informatics system for quantitative community proteomics.
Wang Y, Ahn TH, Li Z, Pan C.
Bioinformatics. 2013 Aug 15;29(16):2064-5. doi: 10.1093/bioinformatics/btt329.

ProtViz 0.6.8 – Proteomics Data Analysis & Visualization

ProtViz 0.6.8

:: DESCRIPTION

protViz is an R package that helps with quality checks, vizualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do solid data analysis for small scale data sets.

::DEVELOPER

The Functional Genomics Center Zurich (FGCZ)

:: SCREENSHOTS

n/a

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • R package

:: DOWNLOAD

 ProtViz

:: MORE INFORMATION

SimGlycan 5.94 – Glycan & Glycopeptide MS/MS Data Analysis Tool

SimGlycan 5.94

:: DESCRIPTION

SimGlycan® predicts the structure of glycans and glycopeptides using mass spectrometry data. SimGlycan® accepts the experimental MS/MS data generated by a mass spectrometer, matches them with its own database of theoretical fragments and generates a list of probable candidate structures.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimGlycan Demo

:: MORE INFORMATION

Order SimGlycan

KegArray 1.2.4 – Microarray Data Analysis & Cluster

KegArray 1.2.4

:: DESCRIPTION

KegArray is a Java application that provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). Tightly integrated with the KEGG database, KegArray enables you to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps.

::DEVELOPER

Kanehisa Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

KegArray

:: MORE INFORMATION

Citation

Methods Mol Biol. 2012;802:19-39.
The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.
Kotera M, Hirakawa M, Tokimatsu T, Goto S, Kanehisa M.