Search Results for "pcr analysis"
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Showing 19 open source projects for "pcr analysis"
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DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. -
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OligoYap Portable
Oligo design and bioinformatic analysis software.
OligoYap can be used to design classical PCR, SYBR Green, TaqMan, MGB, Molecular Beacons, Microarray and Real-Time PCR primers/probes and for bioinformatics analysis. It has the features of enzyme cut analysis, mutation analysis, DNA/protein match and BLAST. You can easily record laboratory materials/files, prepare PCR mix and many other laboratory operations. It works on windows8.1 and earlier operating systems, but has not been tried on windows10 and later. ... -
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covid19
Tokyo COVID-19 Task Force website
New coronavirus infectious disease control site. In Tokyo, in order to centrally announce the infection status in Tokyo, we received reports of outbreaks not only in the jurisdiction of the Tokyo Health Center but also in the cities with health centers (Machida City, Hachioji City) and 23 wards, and aggregated these. In Tokyo, we have set seven monitoring items for the new coronavirus infection, with the two pillars of "infection status" and "medical care provision system" in Tokyo. Every... -
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GMATA software for Genomic SSR marker
Genome-wide Microsatellite Analyzing Toward Application: GMATA
What is software GMATA v21 Genome-wide Microsatellite Analyzing Toward Application (GMATA) is a software for Simple Sequence Repeats (SSR) analyses, and SSR marker designing and mapping in any DNA sequences. It has the following functions: 1. SSR mining; 2. Statistical analysis and plotting; 3. SSR loci graphic viewing; 4. Marker designing; 5. Electronic mapping and marker transferability investigation. GMATA is accurate, sensitive and fast. It was designed to process large genomic... -
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WellMeth
Genome-Wide DNA Methylation Analysis with RRBS
WellMeth is a integrated framework for Reduced Representation Bisulfite-Seq analysis -
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MT-Toolbox
Software for molecule tagged DNA sequences
MT-Toolbox is a user friendly software package for analysis of molecule tagged Illumina MiSeq reads. Molecule tagging is a molecular biology technique to significantly reduce amplicon sequence error and PCR bias which can be applied to any amplicon sequencing project. MT-Toolbox converts raw reads into high quality consensus sequences based on each reads molecule tag. For details and other important information please refer to the MT-Toolbox webpage below. -
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MSP-HTPrimer
A high-throughput primer design tool for DNA methylation analysis
MSP-HTPrimer is an open source, web-based high-throughput and genome-wide primer design pipeline for bisulfite-based assays (MSP, BSP and COBRA) and MSRE-PCR assay and capable of simultaneously processing hundreds to thousands of target sequences. MSP-HTPrimer takes genome-wide annotations of SNPs and repeats into consideration to design primer pairs for higher success rate. MSP-HTPrimer enables hierarchical filtering and visualisation of designed primers in UCSC genome browser for efficient... -
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dpcReport
Standalone GUI for dPCR experiments
Standalone GUI for dPCR experiments. This application launches a graphical user interface that generates reports from digital PCR data. -
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Lab Studies
Rediscover the Simplicity http://www.atgclabs.com/
...The Animal Studies module provides storage for the genotype information, organise genotyping protocols and archive genetic marker information, including for example PCR conditions and results. -
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2bRAD-denovo
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
Download the latest updates from https://github.com/z0on/2bRAD_denovo 2bRAD is a method for cost-efficient whole-genome genotyping, described in Wang et al 2012 http://www.nature.com/nmeth/journal/v9/n8/abs/nmeth.2023.html This project is about analyzing 2bRAD data without a genome reference. Scripts and walkthroughs for: - trimming and quality filtering; - removing PCR duplicates; - assembling loci; - calling variants (SNP-wise and haplotype-wise); - recalibrating quality scores based on genotyping replicates; - smart-thinning and final filtering; - quality assessment based on replicates. Also included are walkthroughs for analysis: - computing Weir and Cockerham Fst - BayeScan - ADMIXTURE - fastSTRUCTURE -
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2bRAD-GATK
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
DOWNLOAD THE LATEST UPDATES FROM https://github.com/z0on/2bRAD_GATK 2bRAD is a method for cost-efficient whole-genome genotyping described in Wang et al 2012 http://www.nature.com/nmeth/journal/v9/n8/abs/nmeth.2023.html This project is about analyzing 2bRAD data using a genome reference (could be a species from the same genus). Scripts and walkthrough for: - trimming and quality filtering; - removing PCR duplicates; - mapping to genome reference; - realigning around indels; - base quality score recalibration; - calling variants; - variant quality score recalibration based on genotyping replicates; - smart-thinning and final filtering; - quality assessment based on replicates. also included are walkthroughs for analysis: - generating data for genome scans (Fst, BayeScan, pi, Tajima's D, deviations in Linkage Disequilibrium) - ADMIXTURE -
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CIMS
Crosslinking induced mutation site analysis
This package includes the scripts to detect statistically reproducible crosslinking induced mutation sites (CIMS) and cross linking induced truncation sites (CITS) from HITS-CLIP data. References: Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293. Zhang,C.†, Darnell, R.B.† 2011.... -
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
DEW is a platform that allows users to explore RNA-Seq data. A web-based Graphical User Interface is included. The analysis proceeds as such: gapped alignments are performed and corrected for length, PCR and fragment bias so that a Fragment Per (effective) Kilobase per Million of reads (FPKM) is estimated as well as the simpler Reads Per Kb per Million of reads (RPKM). When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm estimates effective expression profiles and a corrected alignment is produced. ... -
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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. -
15
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. -
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SOAPsnp
Soapsnp in house version, multi-thread and bam format supported.
...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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DETCT
Differential Expression Transcript Counting Technique pipeline
...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 to be differentiated is high. One extremely useful but underused method for this purpose is the multiplex pyrosequencing technique. mPSQed is a program developed at the Robert Koch Institute and targeted at facilitating the creation of such assays. -
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A simple Java application for the analysis and identification of gene networks. ProPesca takes as input shorts temporal series of realtime-PCR expression levels and it clusters genes that exhibit either similar or specular behaviors.
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