CSGM Designer – Cross Species Genic Marker Designer

CSGM Designer

:: DESCRIPTION

CSGM Designer has been developed with purposes of facilitating easy and systematic design of cross-species genic markers.

::DEVELOPER

CSGM Designer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.
Kim JH, Lee C, Hyung D, Jo YJ, Park JS, Cook DR, Choi HK.
Plant Methods. 2015 Apr 18;11:30. doi: 10.1186/s13007-015-0074-6.

chipPCR 1.0-2 – Toolkit of helper Functions to pre-process Amplification data

chipPCR 1.0-2

:: DESCRIPTION

The chipPCR package is a toolkit of functions to preprocess amplification curve data.

::DEVELOPER

Stefan Roediger [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

chipPCR

:: MORE INFORMATION

Citation:

chipPCR: an R package to pre-process raw data of amplification curves.
Rödiger S, Burdukiewicz M, Schierack P.
Bioinformatics. 2015 Apr 24. pii: btv205.

GPLVM – Time-structured Gene-expression data

GPLVM

:: DESCRIPTION

GPLVM (Gaussian Process Latent Variable Models) is a novel framework to analyse single-cell qPCR expression data from differnt developmental stages.

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
MatLab

:: DOWNLOAD

GPLVM

:: MORE INFORMATION

Citation

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst.
Buettner F, Theis FJ.
Bioinformatics. 2012 Sep 15;28(18):i626-i632. doi: 10.1093/bioinformatics/bts385.

PrimerSeq 1.1.12 – Primer Seek in RNA-Seq

PrimerSeq 1.1.12

:: DESCRIPTION

PrimerSeq designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data.

::DEVELOPER

Xing Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/MacOsX

:: DOWNLOAD

PrimerSeq

:: MORE INFORMATION

Citation

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.
Tokheim C, Park JW, Xing Y.
Genomics Proteomics Bioinformatics. 2014 Apr;12(2):105-9. doi: 10.1016/j.gpb.2014.04.001.

Disperse 1.0.3 – Design of Selector Assays for Targeted Resequencing Applications

Disperse 1.0.3

:: DESCRIPTION

The Disperse project aims to develop and distribute software and data for design of selector assays for exon resequencing applications. The software consists of Java and Perl code integrated into a pipeline that performs all tasks required to transform a list of gene names to a set of selector probes targetting all exonic regions of those genes

::DEVELOPER

Disperse Team

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows / Linux
Java
Perl
Blast

:: DOWNLOAD

Disperse

:: MORE INFORMATION

Citation

J. Stenberg, M. Zhang and H. Ji
Disperse–a software system for design of selector probes for exon resequencing applications
Bioinformatics (2009) 25(5): 666-667

unifiedWMWqPCR 1.28.0 – Unified Wilcoxon-Mann Whitney Test for testing differential Expression in qPCR data

unifiedWMWqPCR 1.28.0

:: DESCRIPTION

unifiedWMWqPCR implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

::DEVELOPER

Jan R. De Neve & Joris Meys <Joris.Meys at UGent.be>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R package
BioConductor

:: DOWNLOAD

unifiedWMWqPCR

:: MORE INFORMATION

Citation

unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R.
De Neve J, Meys J, Ottoy JP, Clement L, Thas O.
Bioinformatics. 2014 May 2. pii: btu313.

Primegens 2.0.5 – Primer Design for Microarray

Primegens 2.0.5

:: DESCRIPTION

Primegens ((PRIMEr Design Using GEN Specific Fragments) is a software for high-throughput primer and probe design. The program uses two third party executables like Primer3 and Megablast.

::DEVELOPER

Primegens Team

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows

:: DOWNLOAD

Primegens

:: MORE INFORMATION

Citation

Gyan Prakash Srivastava, Juyuan Guo, Huidong Shi and Dong Xu.
” PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation pattern of CpG island“.
Bioinformatics 2008 24(17):1837-42.

Beacon Designer 8.21 – Automate Real Time PCR Primer & Probe Design

Beacon Designer 8.21

:: DESCRIPTION

Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

Beacon Designer Demo

:: MORE INFORMATION

ReadqPCR / NormqPCR 1.38.0 / – Read qPCR data / Functions for Normalisation of RT-qPCR data

ReadqPCR / NormqPCR 1.38.0

:: DESCRIPTION

ReadqPCR and NormqPCR are R/Bioconductor packages to analyse RT-qPCR data.

::DEVELOPER

James Perkins <j.perkins at ucl.ac.uk>, Matthias Kohl, Nor Izayu Abdul Rahman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R
BioConductor

:: DOWNLOAD

ReadqPCR and NormqPCR

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Jul 2;13:296. doi: 10.1186/1471-2164-13-296.
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.
Perkins JR1, Dawes JM, McMahon SB, Bennett DL, Orengo C, Kohl M.

CloningBench 3.2.0 – Guide of Cloning Experiments for iPhone / iPAD

CloningBench 3.2.0

:: DESCRIPTION

The CloningBench mobile app is designed to provide you with useful and essential tools to help guide your cloning experiments.

:DEVELOPER

Thermo Fisher Scientific Inc.

:: SCREENSHOTS

:: REQUIREMENTS

iPhone / iPod touch / iPad

:: DOWNLOAD

CloningBench

:: MORE INFORMATION