nondetects 2.16.0 – Model and Impute non-detects in qPCR data

nondetects 2.16.0

:: DESCRIPTION

nondetects is a suit of methods to model and impute non-detects in the results of qPCR experiments.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 nondetects

:: MORE INFORMATION

Citation

On non-detects in qPCR data.
McCall MN, McMurray HR, Land H, Almudevar A.
Bioinformatics. 2014 Apr 23. pii: btu239

Monocle 3 0.2.0 – Differential Expression and Time-series analysis for Single-cell RNA-Seq and qPCR Experiments

Monocle 3 0.2.0

:: DESCRIPTION

Monocle is a toolkit for analyzing single-cell gene expression experiments. It was designed for RNA-Seq, but can also work with single cell qPCR. It performs differential expression analysis, and can find genes that differ between cell types or between cell states. When used to study an ongoing biological process such as cell differentiation, Monocle learns that process and places cells in order according to their progress through it. Monocle finds genes that are dynamically regulated during that process.

::DEVELOPER

Trapnell Lab at the University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 Monocle

:: MORE INFORMATION

Citation

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.
Nat Biotechnol. 2014 Apr;32(4):381-6. doi: 10.1038/nbt.2859.

MRPrimerW – Search valid Primers for multiple Targets of qPCR experiments without matching Off-targets

MRPrimerW

:: DESCRIPTION

The MRPrimerW server performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user.

::DEVELOPER

Infolab DGIST.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MRPrimerW

:: MORE INFORMATION

Citation

MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.
Kim H, Kang N, An K, Koo J, Kim MS.
Nucleic Acids Res. 2016 May 6. pii: gkw380.

ReadqPCR 1.14.0 / NormqPCR 1.14.0 – Read qPCR data / Functions for Normalisation of RT-qPCR data

ReadqPCR 1.14.0 / NormqPCR 1.14.0

:: 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.

unifiedWMWqPCR 1.4.0 – Unified Wilcoxon-Mann Whitney Test for testing differential Expression in qPCR data

unifiedWMWqPCR 1.4.0

:: 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.

MIQE qPCR 1.6 – Check qPCR Experiments

MIQE qPCR 1.6

:: DESCRIPTION

MIQE qPCR helps you in reviewing scientific works and checking your own experiments, when qPCR is involved. Check your project’s compliance to MIQE in minutes, have all required references to hand, and follow qPCR events and news.

::DEVELOPER

LaSalle Beauvais

:: SCREENSHOTS

MIQEqPCR

:: REQUIREMENTS

  • iPhone /  iPad

:: DOWNLOAD

 MIQE qPCR

:: MORE INFORMATION

PrimerPy 0.97a – GUI tool for QPCR Primer Design

PrimerPy 0.97a

:: DESCRIPTION

PrimerPy is a GUI tool for optimal SG QPCR primer design. This branch, Huckleberry, uses “Primer3” as backend engine. The design’s been validated by laboratory experiences; also applicable to conventional PCR.

::DEVELOPER

Suzhao Li

:: SCREENSHOTS

PrimerPy

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PrimerPy

:: MORE INFORMATION

QPCR 1.0 – Store, Manage, and Analyze data from qPCR Experiments

QPCR 1.0

:: DESCRIPTION

QPCR is a versatile web-based Java application that allows to store, manage, and analyze data from quantitative real-time polymerase chain reaction (qPCR) experiments. It comprises a parser to automatically import generated data from qPCR devices and includes a variety of analysis methods to calculate Ct and amplification efficiency values. The analysis pipeline includes technical and biological replicate handling, incorporates sample or gene specific efficiency, normalization using single or multiple housekeeping genes, inter-run calibration, and fold change calculation. Moreover, the application supports proper error propagation throughout all analysis steps and allows conducting statistical tests on sample classes. Results can be visualized in highly customizable charts and exported for further investigation.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

 QPCR

:: MORE INFORMATION

Citation

Pabinger S, Thallinger GG, Snajder R, Eichhorn H, Rader R, Trajanoski Z.
QPCR: Application for real-time PCR data management and analysis.
BMC Bioinformatics 2009, 10:268

PCRsetup – Tool for Planning PCR and qPCR Reactions

PCRsetup

:: DESCRIPTION

PCRsetup is a tool for planning PCR and qPCR reactions, mixing solutions. The higher quality of primers is help to save PCR efficiency at changing PCR conditions. PCR reaction can set up in room temperature and performed without hot-start enzymes.

::DEVELOPER

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PCRsetup

:: MORE INFORMATION

Citation

Kalendar R, Lee D, Schulman AH 2011.
Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Genomics, 97(7).