SPIA 1.1.0 – SNP Panel Identification Assay

SPIA 1.1.0

:: DESCRIPTION

SPIA is a genetic-based assay for the identification of cell lines

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOSX
  • R

:: DOWNLOAD

 SPIA

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2008 Apr;36(7):2446-56. doi: 10.1093/nar/gkn089. Epub 2008 Feb 27.
SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines.
Demichelis F1, Greulich H, Macoska JA, Beroukhim R, Sellers WR, Garraway L, Rubin MA.

qRTDesigner 1.2 – Designing Primers for Real-time Quantitative PCR Assays

qRTDesigner 1.2

:: DESCRIPTION

qRTDesigner is a program for designing primers for real-time quantitative PCR assays.

:DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2015 Apr 8;10(4):e0122713. doi: 10.1371/journal.pone.0122713. eCollection 2015.
Haplotype phasing and inheritance of copy number variants in nuclear families.
Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M

SingleCellAssay 1.0.1 – Infrastructure and Tools for Single Cell Assay Analysis

SingleCellAssay 1.0.1

:: DESCRIPTION

SingleCellAssay is a suit of tools and methods for analysis of single cell assay data in R

::DEVELOPER

RGLAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R

:: DOWNLOAD

 SingleCellAssay

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):461-7. doi: 10.1093/bioinformatics/bts714. Epub 2012 Dec 24.
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.
McDavid A1, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS, Roederer M, Gottardo R.

MRMPlusGUI 20151104 – Quality Control and Assessment tool for SRM/MRM Assay development

MRMPlusGUI 20151104

:: DESCRIPTION

MRMPlusGUI is a freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays.

::DEVELOPER

MRMPlusGUI team

:: SCREENSHOTS

MRMPlus

:: REQUIREMENTS

  • MacOsX/Linux / Windows
  • Java

:: DOWNLOAD

 MRMPlusGUI

:: MORE INFORMATION

Citation

MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.
Aiyetan P, Thomas SN, Zhang Z, Zhang H.
BMC Bioinformatics. 2015 Dec 12;16(1):411. doi: 10.1186/s12859-015-0838-z.

CFAssay 1.4.0 – Statistical analysis for the Colony Formation Assay

CFAssay 1.4.0

:: DESCRIPTION

CFAssay provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.

::DEVELOPER

Herbert Braselmann <braselm at helmholtz-muenchen.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • R/ Bioconductor

:: DOWNLOAD

 CFAssay

:: MORE INFORMATION

Citation

CFAssay: statistical analysis of the colony formation assay.
Braselmann H, Michna A, Heß J, Unger K.
Radiat Oncol. 2015 Nov 4;10(1):223. doi: 10.1186/s13014-015-0529-y.

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

ThermonucleotideBLAST 2.01 – Searching Nucleic Acid-based Assays against Sequence Databases

ThermonucleotideBLAST 2.01

:: DESCRIPTION

ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query.

::DEVELOPER

Jason D. Gans

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

  ThermonucleotideBLAST

:: MORE INFORMATION

WASP – Web-based Allele-Specific PCR Assay designing tool

WASP

:: DESCRIPTION

WASP is an application that designs allele-specific (AS) primers for detecting SNPs and mutations. WASP input can be either key searches (Section A) or SNPs with flanking sequences (Section B). Users can input key searches (SNP IDs or Gene Names), consequently, WASP returns the search result as a graphical interface including SNP information, AS primers (if exist) and PCR condition. SNPs with flanking sequences can be input to the system via the text box or the file uploading module. Additionally, users are able to adjust some primer picking parameters based on the desired PCR condition (Section C).

::DEVELOPER

Genome Institute, BIOTEC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2007 Aug 14;8:275.
WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations.
Wangkumhang P1, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S.

MethMarker 1.0.680 – Facilitate Design of DNA Methylation Assays

MethMarker 1.0.680

:: DESCRIPTION

MethMarker facilitates the design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.

::DEVELOPER

Peter SchüfflerChristoph BockThomas Mikeska and Thomas Lengauer , Max-Planck-Institut Informatik

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 MethMarker

:: MORE INFORMATION

Citation:

MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays
Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock
Genome Biology 2009, 10:R105doi:10.1186/gb-2009-10-10-r105

fitTetra 1.0 – Genotype Calling of Tetraploid Samples based on bi-allelic Marker Assays

fitTetra 1.0

:: DESCRIPTION

fitTetra is an R package for genotype calling of tetraploid samples based on bi-allelic marker assays such as Illumina GoldenGate, Infinium and KASPar. The main characteristic of such assays is that they produce two signals for a sample for a given marker, one signal for each of the two alleles.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 fitTetra

:: MORE INFORMATION

Citation:

Voorrips RE, Gort G, Vosman B (2011)
Genotype calling in tetraploid species from bi-allelic marker data using mixture models.
BMC Bioinformatics 2011, 12:172;