JAMIE 0.91 – Joint Analysis of Multiple ChIP-chip Experiments

JAMIE 0.91

:: DESCRIPTION

JAMIE (Joint Analysis of Multiple IP Experiments) is a R package to perform the joint analysis. The genome is assumed to consist of background and potential binding regions (PBRs). PBRs have context-dependent probabilities to become bona fide binding sites in individual datasets. This model captures the correlation among datasets, which provides basis for sharing information across experiments. Real data tests illustrate the advantage of JAMIE over a strategy that analyzes individual datasets separately.

::DEVELOPER

Ji Lab
:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

JAMIE

:: MORE INFORMATION

Citation

Wu H. and Ji H. (2010)
JAMIE: Joint analysis of multiple ChIP-chip experiments.
Bioinformatics (2010) 26 (15): 1864-1870.

SBEAMS 0.22.1 – Systems Biology Experiment Analysis Management System

SBEAMS 0.22.1

:: DESCRIPTION

SBEAMS is a framework for collecting, storing, and accessing data produced by a wide variety of experiments. The software provides a customizable framework to meet the needs of modern systems biology research.

SBEAMS – Microarray provides MIAME-compliant Affymetrix GeneChip microarray database functionality under the SBEAMS framework.

SBEAMS-Proteomics is part of the SBEAMS (Systems Biology Experiment Analysis Management System) Project, which is a framework for collecting, storing, and accessing data produced by a variety of different experiments; these experiments can be managed separately but then correlated later under the same framework.

::DEVELOPER

SBEAMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • MySQL

:: DOWNLOAD

  SBEAMS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jun 6;7:286.
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology.
Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T.

Well Layout 1.2.1 – Describe 96-Well Experiment

Well Layout 1.2.1

:: DESCRIPTION

The Well Layout program lets you describe a 96-well experiment using a graphical user interface.Layouts (and object in them) can be stored in a persistent Postgres SQL database or they can be stored in CSV-format files on a local hard drive.

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Well Layout

:: MORE INFORMATION

Scotty – Power Analysis for RNA Seq Experiments

Scotty

:: DESCRIPTION

Scotty is a tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • MatLab

:: DOWNLOAD

 Scotty

:: MORE INFORMATION

Citation

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.
Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT.
Bioinformatics. 2013 Mar 1;29(5):656-7. doi: 10.1093/bioinformatics/btt015. Epub 2013 Jan 12.

Flux Simulator 1.2.1 – Modeling RNA-Seq Experiments

Flux Simulator 1.2.1

:: DESCRIPTION

The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts.

::DEVELOPER

Micha Sammeth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Flux Simulator

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Nov 1;40(20):10073-83. doi: 10.1093/nar/gks666. Epub 2012 Sep 7.
Modelling and simulating generic RNA-Seq experiments with the flux simulator.
Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.

Virtual NMJ 2.1.9 – Simulation of an Experiment Recording the Electrical Potentials

Virtual NMJ 2.1.9

:: DESCRIPTION

The Virtual NMJ is a simulation of an experiment recording the electrical potentials associated with neuromuscular transmission at the skeletal neuromuscular junction. The simulation allows you to observe the muscle action potential (AP) and endplate potentials (EPPs) evoked by either nerve stimulation or by direct current stimulation of the muscle fibre. The effects of a variety of drugs and of changes to ionic composition of the extracellular solution on the AP and EPPs can be studied.

::DEVELOPER

the Strathclyde Institute of Pharmacy and Biomedical Sciences

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  Virtual NMJ

:: MORE INFORMATION

MARQ – Mine GEO for Experiments with Similar or opposite Gene Expression Signatures

MARQ

:: DESCRIPTION

MARQ (Microarray Rank Query) is an online microarray retrieval tool based on rank statistics. Datasets in MARQ, most of them retrieved from GEO, are processed into signatures, which are lists of genes ranked by their level of differential expression. Each dataset defines one of more of these signatures based on the possible comparisons of its constituent samples.

::DEVELOPER

MARQ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Vazquez, M., Nogales-Cadenas, R., Arroyo, J., Botías, P., García, R., Carazo, J. M., Tirado, F., Pascual-Montano, A. Carmona-Saez, P. 2010,
`MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.’ ,
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W228-32.

MetaPepSeq 0.8 Beta – Protein Identification in Mass Spectrometry Experiments.

MetaPepSeq 0.8 Beta

:: DESCRIPTION

MetaPepSeq is metaserver for protein identification in Mass Spectrometry Experiments. It helps joining the power of Mascot and de novo sequencing algorithms by merging together into one tool.

::DEVELOPER

CompBio@MIMUW

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 MetaPepSeq

:: MORE INFORMATION

SULDEX 0.01 – Simultaneous Ultra high throughput Ligand Dissociation EXperiment

SULDEX 0.01

:: DESCRIPTION

The SULDEX packages is designed to use high throughput sequencing to simultaneously analyze binding dissociation constants for large repertoires of sequences.

::DEVELOPER

Pollock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SULDEX

:: MORE INFORMATION

Citation

PLoS One. 2011;6(11):e26105. doi: 10.1371/journal.pone.0026105. Epub 2011 Nov 1.
Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.
Pollock DD, de Koning AP, Kim H, Castoe TA, Churchill ME, Kechris KJ.

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