Search Results for "pcr" - Page 2
Sort By:
Showing 70 open source projects for "pcr"
View related business solutions-
Demo Series - Small Business Backup By VeeamWatch this on-demand demo series and learn how to protect your Microsoft 365 data with clear, simple, actionable steps that are easy to implement for businesses of all sizes.
-
PRTG Catches Network Issues Before They Cause DowntimeReactive troubleshooting usually means hearing about a problem from frustrated users, not your monitoring tool. PRTG sets threshold-based alerts across devices, servers and applications, notifying your team by email, SMS or push the moment a metric crosses a set limit. That means catching a failing disk or overloaded server before it becomes an outage and getting time back from firefighting. Start a free trial and set your first alerts today.
-
1
ClinQC
ClinQC: A tool for quality control of Sanger and NGS data in clinic
...It can analyze raw sequencing data and produces unified output as FASTQ files per sample/patient with Sanger quality encoding. First, ClinQC convert input read files from their native formats to a common FASTQ format and remove adapters, and PCR primers. Next, it split barcoded samples, filter duplicates, contamination and low quality sequences and generates a QC report. -
2
Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
-
3
pyQPCR is a GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu
-
4
PCRater
Automatic assessment of PCR assays.
PCRater is a GUI-based tool for a regular, automatic assessment of PCR assays. -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
5
Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. Primers may be designed using information from any of the UCSC hosted genomes... -
6
MLSTEZ is designed for next generation sequencing technology (PacBio CCS or Roche 454 platform) based MSLT methods. MLSTEZ, can automatically identify the barcodes and primers used in the PCR reaction, corrects sequencing errors, generates the MLST profile for each isolate, predicts the potential heterozygous locus, and outputs different alleles. Now ver2.0 supports asymmetric barcode design, please check manual for more details.
-
7
InMethyl
Design of target-specific primers for bis. sequencing of CpG-islands
InMethyl is a Python-based application for the design of target-specific primer combinations for PCR amplification and bisulfite sequencing of complete CpG-islands. InMethyl uses bowtie high-throughoutput aligner to identify potential mis-priming sites in the bisulfite treated or intact genome and then – undesirable potential PCR products. InMethyl provides a balance between various characteristics that allows to pick up primers in hard-to-study genomic regions. -
8
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.... -
9
MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
Earn up to 16% annual interest with Nexo.Generate interest, borrow against your crypto, and trade a range of cryptocurrencies — all in one platform. Geographic restrictions, eligibility, and terms apply.
-
10
simulate_pcr
PCR target prediction software
Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. This script predicts potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch tolerance and amplicon length range to be set by the user. The PCR amplicon simulation code also annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons. ... -
11
RErun
Create virtual DNA/RNA agarose gels
RERun is a software tool for creating virtual agarose electrophoresis gels of nucleic acid fragments (restriction digests, PCR amplicons, etc). It is written in Perl and developed on Linux, although it can be made to run on Windows with some work (undocumented). -
12
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. ... -
13
PriMux is a k-mer based library for genomic investigations, and for development of PCR signatures that may include degenerate base pairs
-
14
adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. ... -
15
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. -
16
Allele Builder
python-based tool for multi-allele gene analysis
...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. -
17
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.
-
18
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. -
19
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 are queried from existing online tools with BatchPD acting as an intermediate to handle queries and results processing. ... -
20
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. -
21
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. -
22
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).
-
23
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.
-
24
PhiSiGnS: a tool to identify signature genes in phages and design PCR primers for examining phage diversity
-
25
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.
