PhosphoSiteAnalyzer 1.4 – Bioinformatical tool for Analyzing (Quantitative) Phosphoproteome datasets

PhosphoSiteAnalyzer 1.4

:: DESCRIPTION

PhosphoSiteAnalyzer is a novel bioinformatical tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN (Linding et al) and contains various statistical modules for futher analysis.

::DEVELOPER

PhosphoSiteAnalyzer team

:: SCREENSHOTS

PhosphoSiteAnalyzer

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  PhosphoSiteAnalyzer

:: MORE INFORMATION

Citation

PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN.
Bennetzen MV, Cox J, Mann M, Andersen JS.
J Proteome Res. 2012 Jun 1;11(6):3480-6. doi: 10.1021/pr300016e.

Oqtans 0.1 beta – Online Quantitative Transcriptome Analysis

Oqtans 0.1 beta

:: DESCRIPTION

Oqtans is an integrative online platform for quantitatively analyzing RNA-Seq experiments. It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis

::DEVELOPER

Rätsch Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Oqtans

:: MORE INFORMATION

Citation:

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.
Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G.
Bioinformatics. 2014 May 1;30(9):1300-1. doi: 10.1093/bioinformatics/btt731.

MAPDIA 2.0.0 – Model-based Analysis of quantitative Proteomics data in DIA-MS

MAPDIA 2.0.0

:: DESCRIPTION

mapDIA performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs.

::DEVELOPER

MAPDIA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 MAPDIA

:: MORE INFORMATION

Citation

mapDIA: Preprocessing and Statistical Analysis of Quantitative Proteomics Data from Data Independent Acquisition Mass Spectrometry.
Teo G, Kim S, Tsou CC, Collins B, Gingras AC, Nesvizhskii AI, Choi H.
J Proteomics. 2015 Sep 14. pii: S1874-3919(15)30130-5. doi: 10.1016/j.jprot.2015.09.013

EBprot 1.1.0 – Bayesian Analysis of labeling-based Quantitative Proteomics Data

EBprot 1.1.0

:: DESCRIPTION

EBprot is a novel probabilistic framework that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides.

::DEVELOPER

EBprot team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Windows
  • R

:: DOWNLOAD

 EBprot

:: MORE INFORMATION

Citation

EBprot: Statistical analysis of labeling-based quantitative proteomics data.
Koh HW, Swa HL, Fermin D, Ler SG, Gunaratne J, Choi H.
Proteomics. 2015 Aug;15(15):2580-91. doi: 10.1002/pmic.201400620.

XiQ 0.1 – Quantitative Cross-linking/Mass Spectrometry

XiQ 0.1

:: DESCRIPTION

XiQ is an open source application to carry out automated quantitation of CLMS (Cross-linking/mass spectrometry) data.

::DEVELOPER

Rappsilber Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

 XiQ

:: MORE INFORMATION

Citation

J Proteomics. 2013 Aug 2;88:120-8. doi: 10.1016/j.jprot.2013.03.005. Epub 2013 Mar 26.
Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers.
Fischer L1, Chen ZA, Rappsilber J.

hapQTL 0.99 – Haplotype Quantitative Loci

hapQTL 0.99

:: DESCRIPTION

hapQTL performs association testing between local haplotypes and phenotypes at each core marker.

::DEVELOPER

Yongtao Guan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

 hapQTL

:: MORE INFORMATION

Citation

Genetics. 2014 Jul;197(3):823-38. doi: 10.1534/genetics.114.164814. Epub 2014 May 8.
Detecting local haplotype sharing and haplotype association.
Xu H, Guan Y

E-MAPs 1.1 – Imputing Quantitative Genetic Interactions

E-MAPs 1.1

:: DESCRIPTION

E-MAPs (Epistatic miniarray profiles) are a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values – up to 35% – that can reduce the effectiveness of some data analysis techniques and prevent the use of others.

::DEVELOPER

Colm Ryan  (colm.ryan@ucd.ie)  @ the Machine Learning Group (MLG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Python

:: DOWNLOAD

 E-MAPs

:: MORE INFORMATION

Citation

Missing value imputation for epistatic MAPs
Colm Ryan , Derek Greene , Gerard Cagney and Pádraig Cunningham
BMC Bioinformatics 2010, 11:197 doi:10.1186/1471-2105-11-197

EasyFRAP – Quantitative and Qualitative Analysis of FRAP data

EasyFRAP

:: DESCRIPTION

EasyFRAP assists quantitative and qualitative analysis of FRAP data.The user can handle simultaneously large datasets of raw data, visualize fluorescence recovery curves, exclude low quality data, perform data normalization, extract quantitative parameters, perform batch analysis and save the resulting data and figures for further analysis.

::DEVELOPER

the Cell Cycle Laboratory at the School of Medicine, University of Patras.

:: SCREENSHOTS

EasyFRAP

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 EasyFRAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1800-1. doi: 10.1093/bioinformatics/bts241. Epub 2012 Apr 27.
easyFRAP: an interactive, easy-to-use tool for qualitative and quantitative analysis of FRAP data.
Rapsomaniki MA1, Kotsantis P, Symeonidou IE, Giakoumakis NN, Taraviras S, Lygerou Z.

L-Measure 5.2 – Extract quantitative Morphological Measurements from Neuronal Reconstructions

L-Measure 5.2

:: DESCRIPTION

L-Measure allows researchers to extract quantitative morphological measurements from neuronal reconstructions. Neuronal reconstructions are typically obtained from brightfield or fluorescence microscopy preparations using applications such as Neurolucida, Eutectic, or Neuron_Morpho, or can be synthesized via computational simulations. Several hundreds neuronal reconstructions are freely available to the neuroscience community (via web archives and peer-to-peer exchange) from a dozen of laboratories.

::DEVELOPER

Sridevi Polavaram

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

  L-Measure

:: MORE INFORMATION

Citation:

Scorcioni R., Polavaram S., Ascoli G.:
L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies.
Nature Prot. 3:866-76 (2008).

TotalLab Quant 12 – Analysis Tools for Quantitative Image Analysis

TotalLab Quant 12

:: DESCRIPTION

TotalLab Quant is a suite of core analysis tools for quantitative image analysis applications in the Life Sciences.

::DEVELOPER

TotalLab Limited

:: SCREENSHOTS


:: REQUIREMENTS

  • Windows

:: DOWNLOAD

TotalLab Quant

:: MORE INFORMATION