Search Results for "pcr" - Page 3
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Showing 90 open source projects for "pcr"
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Red Hat Enterprise Linux (RHEL) on Microsoft Azure provides a secure, reliable, and flexible foundation for your cloud infrastructure. Red Hat Enterprise Linux on Microsoft Azure is ideal for enterprises seeking to enhance their cloud environment with seamless integration, consistent performance, and comprehensive support.
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ConnectWise ScreenConnect, formerly ConnectWise Control, is a remote support solution for Managed Service Providers (MSP), Value Added Resellers (VAR), internal IT teams, and managed security providers. Fast, reliable, secure, and simple to use, ConnectWise ScreenConnect helps businesses solve their customers' issues faster from any location. The platform features remote support, remote access, remote meeting, customization, and integrations with leading business tools.
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PriMux is a k-mer based library for genomic investigations, and for development of PCR signatures that may include degenerate base pairs
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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Allele Builder
python-based tool for multi-allele gene analysis
Allele Builder aims at analysis of multi-allele and multi-locus genes as well as microbiome study. In contrast to the other software enabling 454 data prcessing the Allele Builder allows the usage of long amplicons with two-tailed reads. Allele Builder effectively eliminates chimeric reads coming from artificial recombination between two PCR amplicons. -
Out-of-the-box scripts. Around-the-clock monitoring. Unmatched automation capabilities. Start doing more with less and exceed service delivery expectations.
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Mutascope
Analysis software designed for PCR-amplicon sequencing data.
Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. -
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estMOI
estimating Multiplicity Of Infection using short read sequence data
estMOI is intended to estimate Multiplicity of Infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data as follows: INPUT files: estMOI requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. 1. Short reads are aligned to a reference genome using... -
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A set of utilities for generating and analyzing PCR primers. Primers can be designed against target and 'exclude' databases and optimized to reduce secondary structure elements. Output includes publication-quality graphics.
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SOAPsnp
Soapsnp in house version, multi-thread and bam format supported.
... Duo genotyping sites shows great accuracy. Over 99% of the genotyping sites are covered at over 99.9% consistency. Further PCR plus Sanger sequencing of the inconsistent SNP sites confirmed majority of the SOAPsnp results. -
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Cy0 Quantification
Algorithm to calculate Cy0 parameter from raw data of real time PCR
The algorithm was writen in MATLAB. It uses raw fluorescent data of real time PCR experiments to determine de Cy0 parameter. More info about Cy0 can ba found in http://www.cy0method.org/. This algorithm enables molecular biologist to evaluate their experiments using Cy0, a parameter more accurate and exact. -
We design our technology to make workforce management easier. APS offers core HR, payroll, benefits administration, attendance, recruiting, employee onboarding, and more.
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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BatchPD
BatchPD: Batch automation of a primer design pipeline for human genes
BatchPD is a primer design program developed to address the needs of clinical diagnostics laboratories to design primer oligos for PCR amplification against human gene exons, taking into account of SNPs where possible. Research paper publication: http://www.bioinformation.net/008/97320630008365.htm BatchPD checks specificity via in-silico PCR, provide gene/exon specific relevant information summarised in an end spread-sheet; Primer design, PCR checks and other relevant information... -
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DETCT
Differential Expression Transcript Counting Technique pipeline
A perl pipeline for identifying differentially expressed genomic regions from transcript counting experiments. The pipeline first uses a Hidden Markov Model (HMM) to identify genomic regions based on the data from the experiment. During the sample counting step the pipeline removes reads which are suspected as being PCR duplicates. The differential expression analysis is currently performed using the DESeq package from Bioconductor. -
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mPSQed
Alignment editor and multiplex pyrosequencing assay designer
Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required for confirmation or typing. The design of appropriate PCR-based assays is a complex task, especially when conserved discriminating polymorphisms are rare or if the number of types which need... -
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pal_finder is a perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads. It then designs PCR primers to amplify these repeat loci (Potentially Amplifiable Loci: PAL).
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PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.
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PhiSiGnS: a tool to identify signature genes in phages and design PCR primers for examining phage diversity
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A RT-PCR data normalization tool that processes RT-PCR data and primer information to make annotation files, and analyzes the data statistically [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)].
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PCR-Virtual v2.0 is a prototype of a Virtual Community Plataform using Master Data Management technology. This version integrates two public databases: CADUNICO (Social information) and SIH (Health information).
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Gepoclu - Gene Positional Clustering is a suite of Matlab functions for performing positional clustering on genes with optional use of expression data such as what can be obtained from Microarray, EST and qRT-PCR, and PCR.
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This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.
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FAS-DPD is a program to design degenerate primers for PCR.
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A batch primer selection program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. BOSS will select oligos for gap closure of both contig and scaffold gaps. See readme for details.