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TOPSI / Tool for PCR Signature Identification
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.
NqA / Normalization qPCR Array
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.
McSNP Base calling / Melting curve Single nucleotide polymorphism Base calling
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.
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