Code for design of diagnostic PCR primers, and metabarcoding markers.

quantitative PCR analysis in the tidyverse

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

Auto-analysis for Real-Time PCR (qPCR) data

OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

Quality assessing, analyzing and testing the statistical significance of real-time quantitative PCR data

A python package to analyse qPCR data for single-use or high-throughput application

RDML data import for R

rdml: Mathematica package for Real-Time qPCR data

Bioinformatics CNV Detection with Random Forest Model

Molecular biology visualization tools for Shiny apps

This repository contains scripts and data for training and utilizing machine learning classifiers to predict qPCR cross-amplification.

Modeling of primers/probes hybridization on to a set of target viral sequences.

Takes excel file output from qPCR (Quantstudio3, ABI) and sample labels. Optionally analyzes standard curves and plots CT, Tms and absolute copies

Technical data sets by Ruijter et al. (2013)

An easy way to normalize CT values to Internal controls as well as housekeeping genes and download as heatmap.

Qupid (Quantitative PCR Interface to Delta-Delta-Ct) - a versatile web-application for swift Delta-Delta-Ct analysis of qPCR data

Biomarker data set by Vermeulen et al. (2009)

Repository for pan-spefic primers designed for tiled full genome sequencing or qPCR of viral pathogens. Pathogens include amongst others Hepatitis E virus, Hepatitis A virus, Poliovirus and SARS-COV-2. Primers were designed with varVAMP.