GenEx 7.0 – Analyze Real-time qPCR Data

GenEx 7.0

:: DESCRIPTION

GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis.

::DEVELOPER

MultiD Analyses AB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GenEx

:: MORE INFORMATION

LinRegPCR 20210614 – Analysis of Quantitative PCR Data

LinRegPCR 20210614

:: DESCRIPTION

LinRegPCR is a program for the analysis of quantitative RT-PCR (qPCR) data resulting from monitoring the PCR reaction with SYBR green or similar fluorescent dyes. The program determines a baseline fluorescence and does a baseline subtraction. Then a Window-of-Linearity is set and PCR efficiencies per sample are calculated. With the mean PCR efficiency per amplicon, the Ct value per sample and the fluorescence threshold set to determnine the Ct, the starting concentration per sample, expressed in arbitrary fluorescence units, is calculated

::DEVELOPER

J. M. Ruijter, S. van der Velden,A. Ilgun @ Heart Failure Research Center (HFRC)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Excel

:: DOWNLOAD

 LinRegPCR

:: MORE INFORMATION

Citation

Ramakers C, Ruijter JM, Deprez RH, Moorman AF. (2003)
Assumption-free analysis of quantitative real-time PCR data
Neurosci Lett 2003 Mar 13;339(1): 62-66

DIVE 1.0 – Data Intensive Visualization Engine

DIVE 1.0

:: DESCRIPTION

DIVE is a software for domain independent analysis of complex data. It is capable of real-time data analysis, ontological data representation, and has an extensible data pipeline. DIVE allows fast and agile access to the Dynameomics data warehouse by interactive graphics, scripted data analysis and direct SQL access.

::DEVELOPER

Daggett Research Group at the University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 DIVE

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 15;30(4):593-5. doi: 10.1093/bioinformatics/btt721. Epub 2013 Dec 13.
DIVE: a data intensive visualization engine.
Bromley D1, Rysavy SJ, Su R, Toofanny RD, Schmidlin T, Daggett V.

Cyber-T – Software and Server for Analysis of DNA Microarray data

Cyber-T

:: DESCRIPTION

Cyber-T is a a microarray analysis web interface from UCI’s Institute for Genomics and Bioinformatics. It accommodates both paired (2-dye) data and data in which control and experiment are on separate experiments (e.g. affymetrix based data). It also supports Bayesian statistical approaches and Bonferroni corrections for significance analysis of differentially expressed clones.

::DEVELOPER

Pierre Baldi and Tony Long at Institute for Genomics and Bioinformatics 

:: REQUIREMENTS

:: DOWNLOAD

 Cyber-T

:: MORE INFORMATION

Citation:

Kayala, M.A. and Baldi, P.,
Cyber-T web server: differential analysis of high-throughput data“,
Nucleic Acids Research, 40 (W1): W553-W559, (2012).

P. Baldi and A.D. Long,
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes“,
Bioinformatics, 17, 6, 509-519, (2001).

HAPSIM – Produce the Case-control Multilocus Genotype Data

HAPSIM

:: DESCRIPTION

HAPSIM is a program for generating case-control multi-locus genotype data under a specified disease model.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HAPSIM

:: MORE INFORMATION

Citation:

B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356

NNPERM 1.3 – Analyse Case-control Multi-locus Genotype Data

NNPERM 1.3

:: DESCRIPTION

NNPERM is a neural network program for analysing case-control multi-locus genotype data using a permutation test.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NNPERM

:: MORE INFORMATION

Citation:

B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356

ArrayExpress 1.52.0 – Functional Genomics data

ArrayExpress 1.52.0

:: DESCRIPTION

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies.

::DEVELOPER

Brazma group at EMBL-EBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 ArrayExpress

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2003 Jan 1;31(1):68-71.
ArrayExpress–a public repository for microarray gene expression data at the EBI.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4. doi: 10.1093/nar/gkq1040. Epub 2010 Nov 10.
ArrayExpress update–an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.

ArrayExpress update—trends in database growth and links to data analysis tools
RUSTICI, G., KOLESNIKOV N., BRANDIZI M., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., ISON J., KEAYS M., et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D987–D990

BRB-ArrayTools 4.6.2 – Visualization & Analysis of DNA Microarray Gene Expression Data

BRB-ArrayTools 4.6.2

:: DESCRIPTION

BRB-ArrayTools is an integrated software package for the analysis of DNA microarray data.

BRB-ArrayTools contains utilities for processing expression data from multiple experiments, visualization of data, multidimensional scaling, clustering of genes and samples, and classification and prediction of samples. BRB-ArrayTools features drill-down linkage to NCBI databases using clone, GenBank, or UniGene identifiers, and drill-down linkage to the NetAffx database using Probeset ids.

::DEVELOPER

the Biometric Research Branch of the Division of Cancer Treatment & Diagnosis of the National Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BRB-ArrayTools

:: MORE INFORMATION

Citation

Analysis of gene expression data using BRB-ArrayTools.
Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y.
Cancer Inform. 2007 Feb 4;3:11-7.

XMRF 1.0 – Fit Markov Networks to High-Throughput Genomics Data

XMRF 1.0

:: DESCRIPTION

XMRF is an R package implemented to enable biomedical researchers to discover complex interaction between genes from multi-dimensional genomics data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

XMRF

:: MORE INFORMATION

Citation

Wan YW, Allen GI, Baker Y, Yang E, Ravikumar P, Anderson M, Liu Z.
XMRF: an R package to fit Markov Networks to high-throughput genetics data.
BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):69. doi: 10.1186/s12918-016-0313-0. PMID: 27586041; PMCID: PMC5009817.

Paxtools 5.1.0 / PaxtoolsR 1.26.0 – Accessing & Manipulating BioPAX Data

Paxtools 5.1.0 / PaxtoolsR 1.26.0

:: DESCRIPTION

Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format. The Paxtools Java programming library for BioPAX has been developed to help software developers readily support the import, export and validation of BioPAX-formatted data for various uses in their software . Using Paxtools, a range of BioPAX-compatible software has been developed, including browsers, visualizers, querying engines, editors and converters

PaxtoolsR provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC).

::DEVELOPER

Computational Biology Center at MSKCC 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java / R/ BioConductor

:: DOWNLOAD

 Paxtools , PaxtoolsR

:: MORE INFORMATION

Citation:

PaxtoolsR: Pathway Analysis in R Using Pathway Commons.
Luna A, Babur Ö, Aksoy BA, Demir E, Sander C.
Bioinformatics. 2015 Dec 18. pii: btv733.

Demir et al.
The BioPAX community standard for pathway data sharing
Nature Biotechnology 28 , 935–942 (2010) doi:10.1038/nbt.1666