Tag: Data Analysis

ProteoWizard 3.0.21193 – Proteomics Data Analysis

ProteoWizard 3.0.21193

:: 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.

ARB 6.0.6 – Sequence Database Handling and data analysis

ARB 6.0.6

:: 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

Prof. Dr. Wolfgang Liebl

:: 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.

Perseus v1.6.15.0 – Shotgun Proteomics Data Analysis

Perseus v1.6.15.0

:: DESCRIPTION

Perseus 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.

CisGenome 2.0 – ChIP-chip and ChIP-seq Data Analysis

CisGenome 2.0

:: DESCRIPTION

CisGenome is a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP–microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information.

::DEVELOPER

Ji Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

CisGenome

:: MORE INFORMATION

Citation

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers and Wing H.Wong (2008)
An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Nature Biotechnology, 26: 1293-1300. doi:10.1038/nbt.1505

RseqFlow 2.2 – RNA-seq Data Analysis Workflow

RseqFlow 2.2

:: DESCRIPTION

RseqFlow is a workflow which can implement a set of RNA-Seq analysis, such as performing quality control (QC) for sequencing data, generating signal tracks of mapped reads, calculating expression levels, and identifying differentially expressed genes. The workflow allows users to express multi-step RNA-Seq analysis by just providing sequencing RNA-Seq datasets and typing a few commands in an easy-to-use environment.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Virtual Machine

:: DOWNLOAD

 RseqFlow

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 15;27(18):2598-600. Epub 2011 Jul 27.
RseqFlow: workflows for RNA-Seq data analysis.
Wang Y, Mehta G, Mayani R, Lu J, Souaiaia T, Chen Y, Clark A, Yoon HJ, Wan L, Evgrafov OV, Knowles JA, Deelman E, Chen T.

CpGviewer 20110406 – Interactive Data Analysis in Bisulphite DNA Sequencing

CpGviewer 20110406

:: DESCRIPTION

CpGviewer is designed to speed up the characterisation of mammalian CpG islands by aligning DNA sequences from bisulphite-modified DNA to the genomic sequence of the CpG island. While simple in principle, this is a tedious error-prone task when done manually

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

CpGviewer

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 CpGviewer

:: MORE INFORMATION

Citation

Carr IM, Valleley EMA, Cordery SF, Markham AF & Bonthron DT (2007).
Sequence analysis and editing for bisulphite genomic sequencing projects.
Nucleic Acids Res., 35:e79.

Arlequin 3.5.2.2 – Population Genetics Data Analysis

Arlequin 3.5.2.2

:: DESCRIPTION

Arlequin is an exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data).

The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Arlequin

:: MORE INFORMATION

Citation

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
Excoffier L, Lischer HE.
Mol Ecol Resour. 2010 May;10(3):564-7. doi: 10.1111/j.1755-0998.2010.02847.x.

Cytobank – Analytics Platform for Community Cytometry Data Analysis

Cytobank

:: DESCRIPTION

Cytobank is a platform that allows researchers to annotate, analyze, and share results along with the underlying single-cell data.

::DEVELOPER

Cytobank Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Curr Top Microbiol Immunol. 2014;377:127-57. doi: 10.1007/82_2014_364.
Cytobank: providing an analytics platform for community cytometry data analysis and collaboration.
Chen TJ1, Kotecha N.

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.