Calls the genotypes of single nucleotide polymorphisms (SNP) from TaqMan allelic discrimination assays. SNPman utilizes the fluorescence data collected over the whole polymerase chain reaction (PCR) run, rather than relying on the end point fluorescence measurements that is the basis of the genotype calling process in most software solutions sold with the real-time instruments. It works with data from three different widely used PCR instruments.
Allows users to predict a number of latent dimensions. GrandPrix assists users in analyzing the single-cell data. This permits researchers to examine the temporal dynamics of complex biological processes where the generation of time course experiments is technically impossible. This approach can reveal interesting biological facts such as identifying branching points in the differentiation pathways.
Contains functions to perform normalization of high-throughput qPCR data. qpcrNorm calculates the coefficient of variation for each gene in the qPCR experiment, and returns the average coefficient of variation across all genes. This software offers two data-driven normalization methods that directly correct for technical variation and represent robust alternatives to standard housekeeping gene-based approaches.
A high-performance computing pipeline for the design of PCR-based pathogen diagnostic assays. The TOPSI pipeline efficiently designs PCR signatures common to multiple bacterial genomes by obtaining the shared regions through pairwise alignments between the input genomes. This pipeline consists of a pre-processing step, a post-processing step, and three different stages. TOPSI extends the Tool for Oligonucleotide Fingerprint Identification (TOFI) framework to design signatures for real-time PCR-based diagnostic assays.
Recognizes a small set of miRNAs to use as reference for data normalization in view of subsequent validation studies. NqA employs high-throughput quantitative real-time polymerase chain reaction (qPCR) data to proceed. It can serve to assess promising miRNAs during the discovery phase based on qPCR high-throughput data. This tool returns frequency distribution of evaluated miRNAs according to the comparison group, a list of the N miRNAs expressed in all the samples.
Serves for quality assessment, analysis and testing of quantitative polymerase chain reaction (qPCR) data. pcr implements two methods for relative quantification of mRNA expression. It can calculate the amplification efficiency and curve from real-time quantitative PCR data. Its main function is to allow users to perform all necessary steps of qPCR analysis and produce graphs in a uniform way.
Highlights differences between bacterial populations. DirtyGenes is useful with different types of data, such as metagenomics data, or quantitative polymerase chain reaction (qPCR) data. This tool is useful for computation number of samples needed in experiments.
Comprises a peak detection procedure and an ordinal regression model. McSNP is a relatively cheap and handy genotyping technique as it is an extension of the reverse transcription-polymerase chain reaction (RT-PCR) technique. It makes use of the difference in melting temperature of PCR products for different alleles. Users and clinicians can conduct the base calling using the default settings directly. A graphical user interface (GUI) is provided for the ease of data manipulation.
Introduces concepts of multi-factorial experimental design and supports teaching of the polymerase chain reaction. PCR Simulator is an on-line application modelled on laboratory protocols for performing the PCR. The software provides a virtual experience of a complex laboratory protocol with the simulated reactions qualitatively matching real experiments. It enables users to generate data for their own analysis within the teaching environment, allowing combined teaching of experimental design and experimental analysis.
A web app to support all PCR-related processes. PCRdrive can find a PCR among thousands of publicly available PCRs into the database, but also permits the design of primers, ordering of reagents and documentation to sharing of PCRs. This tool enables collaboration between researchers and sharing of new PCRs which can be saved into the web app with a documentation.
Generates polymerase chain reaction (PCR) products in overlapping segments to span the entire region from sequence data in FASTA format. PCR-Overlap divides up a given sequence, based on users’ criteria for PCR product size and overlap between adjacent segments, and pass this data to the PCR primer selecting program 'Primer3'.
Automates time-consuming and difficult parts of the polymerase chain reaction (PCR) interpretation process. FastFinder perform standardization of the results and no longer prone to subjectivity. The platform can be linked to any cycler and isn't dependent on a single assay manufacturer. FastFinder can transform lab into an efficiency hub with smart automation. In more, it can speed up real-time PCR and free up time to do more things in just as much time.
Simulates Polymerase chain reaction (PCR) given a list of sequences in FASTA or Genbank format. WebPCR is a web app that simulates PCR given primers and a template sequence. The last sequence in the list is interpreted as template and the preceding ones as primers. For each potential PCR product, a report will be generated containing the PCR product sequence and some additional data. It is a python program running in the cloud on a free Google app engine.
Allows users to give tags. Webtag is based on improved algorithms for tag/anchor generation, much faster runtime and the possibility to handle batch runs. The tags produced are: (1) suitable for a specific organism, and (2) compatible with other oligonucleotides to be used in the experimental procedures. This tool calculates the melting temperature of the sense primer and then queries the database constructed from tags determined by the algorithm.
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