ThermonucleotideBLAST 2.04 – Searching Nucleic Acid-based Assays against Sequence Databases

ThermonucleotideBLAST 2.04

:: 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

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

CFAssay 1.26.0 – Statistical analysis for the Colony Formation Assay

CFAssay 1.26.0

:: 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.

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.

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

PROBer v0.3.1 – Toolkit for Analyzing Sequencing-based ‘Toeprinting’ Assays

PROBer v0.3.1

:: DESCRIPTION

PROBer is the first unified probabilistic framework for the analysis of a diverse set of sequencing-based ‘toeprinting’ assays. These assays are used to probe RNA secondary structure (DMS/SHAPE-Seq), detect epitranscriptomic mark (Pseudo-Seq), or identify RNA-protein interaction (iCLIP/eCLIP), which are important to understanding post-transcriptional gene regulation from all aspects.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

PROBer

:: MORE INFORMATION

Citation

Cell Syst, 4 (5), 568-574.e7 2017 May 24
PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays
Bo Li , Akshay Tambe , Sharon Aviran , Lior Pachter

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.

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;

AssayZap 3.0 – System for Analyzing RIAs, ELISAs, IRMAs and other Assays

AssayZap 3.0

:: DESCRIPTION

AssayZap is a universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay. Counts of up to 2^31 can be handled. Standard curves can be fitted by 2-parameter, 4-parameter or 4-parameter weighted fit, or by the unique interactive manual fit which permits all standard curves to be fitted, whatever their shape. Assays may include up to 2000 tubes and up to four standard curves, each of which can incorporate up to 24 values. Assay drift can be compensated by interpolation of results between standard curves.

::DEVELOPER

Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AssayZap

:: MORE INFORMATION

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