Search Results for "throughput" - Page 13
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Showing 502 open source projects for "throughput"
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NiceShaper - Dynamic Traffic Shaper
NiceShaper provides dynamic traffic shaping for Linux router
...While constantly monitoring the traffic flowing through the router, in response to the changing load, dynamically adjusts the rate and ceil parameters values of enabled HTB classes to the values which enable the fullest possible utilization of Internet connection throughput. NiceShaper protects each host which uses reasonable amount of shared throughput while watching over the configured optimal utilization of Internet connection. Therefore, at the asymmetric Internet connectio -
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Opera
An optimal genome scaffolding program
...Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y. Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170. -
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Identifies rRNA, contaminants, trims in a standard fashion etc. Maintains read pairs. Built for fire-and-forget high throughput projects (terabytes of data). Uses pbzip2, bowtie2, fastx_toolkit, samtools, fastqc, Trimmomatic (optional)
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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 selection of assays. -
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SURCOMED
SUrvival COmbined effect-driven cancer MEchanism Discovery
Survival analyses based on the Kaplan-Meier estimate have been pervasively used to support or validate the relevance of biological mechanisms in cancer research. Recently, with the appearance of gene expression high-throughput technologies, this kind of analysis has been applied to tumour transcriptomics data. In a ‘bottom-up’ approach, gene-expression profiles that are associated with a deregulated pathway hypothetically involved in cancer progression are first identified and then subsequently correlated with a survival effect, which statistically supports or requires the rejection of such a hypothesis. ... -
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QAmiRSeq
A strand aware pipeline for accurate quantification of miRNAs/isomiRs
We designed and implemented a pipeline called QAmiRSeq for fast and accurate quantification of both known miRNAs and isomiRs from high throughput sequencing. QAmiRSeq reconciles its implementation with the unique nature of miRNAs. It is the first algorithm that takes advantage of the strand information for more accurate quantification. All analyses results are organized in a user friendly manner, accessible via a web interface, and can be drilled down interactively by investigators or analysts to conduct further investigation and discovery. ... -
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Hyperic is application monitoring and performance management for virtual, physical, and cloud infrastructures. Auto-discover resources of 75+ technologies, including vSphere, and collect availability, performance, utilization, and throughput metrics.
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MSRE-HTPrimer
A high-throughput primer design tool for MSRE-assay in epigenetics
MSRE-HTPrimer is an open-source, portable, web-based and easy-to-use tool, which facilitates the design of primer pairs for epigenetic assay design and and genomic sequencing assay design. It uses a simple input and output model and can design primers for hundreds to thousands of target sequences in a single run. Moreover, it does not have any limitations on the number and size of target sequences. MSRE-HTPrimer provides significant improvements over existing solutions with following unique... -
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VCF Explorer
A desktop application for analyzing whole genome VCF files
he decreasing cost high-throughput technologies led to a number of sequencing projects consisting thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyze exome files are not adequate for large VCF files produced by whole genome studies. -
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Combenefit
Synergy analyses of drug and other other agent combinations
Combenefit software is a standalone application for Windows that performs surface analyses of drug and other agent combinations to identify synergy. Please cite as: "Di Veroli,G.Y. et al. (2016) Combenefit: an interactive platform for the analysis and visualization of drug combinations. Bioinformatics." (http://bioinformatics.oxfordjournals.org/content/early/2016/05/27/bioinformatics.btw230.abstract) Current version... -
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
This page is here for archival purpose. Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/... -
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MetaOpen
Metabolomics Bioinformatics Tools
Our bioanalytical research exploits practical and efficient high-throughput technologies for the analyses of complex mixtures derived from living systems. This will facilitate the development of preventive, predictive and personalized medicine for specific diseases and will promote health and wellness. We use a number of high-throughput analytical platforms including multidimensional liquid chromatography-mass spectrometry (MDLC-MS) for proteomics, and for metabolomics; liquid chromatography-mass spectrometry (LC-MS), and comprehensive two-dimensional gas chromatography-mass spectrometry (GCxGC/TOF-MS). ... -
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Re-Annotator
Re-annotates Microarray Probes
The microarray technology is an established approach for high throughput gene expression analysis. An accurate mapping between array probes and the genes that they are targeting is essential for generating accurate biological findings. The manufacturers typically provide such annotation tables. However, these tables rely on older genome and transcriptome versions that differ substantially from the current state-of-the-art sequence databases. -
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Bamformatics
Toolkit and GUI for sequencing data analysis
The Bamformatics project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data. Its toolkit includes, among others, programs to identify variants and to compute various types genomic tracks. It also provides a graphical user interface to facilitate general bioinformatic workflows. The project wiki contains further details. -
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ipc-quartztime
inter process communication library based on POSIX
ipc-quartztime is an inter process communication library based on shared memory, mutexes and signals. ipc-quartztime is intended for high-speed and high-throughput communication between processes. -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting in near perfect pre-assembly reads. ... -
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ncmock
NetCDF mock data generator.
...Global and variable attributes can also be created. Esoteric controls exist for choosing alignment, blocksize, file flavor (classic or HDF5), prefill, initial size, and header pad. ncmock has throughput and peak memory calipers, so it can also be used as a benchmark tool -
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HTSeq
Analysing high-throughput sequencing data with Python
This SourceForge page is outdated! HTSeq has been moved to github: https://github.com/simon-anders/htseq General information and documentation on HTSeq; http://www-huber.embl.de/users/anders/HTSeq -
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EDDA
Experiment Design for Differential Abundance Analysis
...EDDA can aid in the design of a range of common experiments such as RNA-seq, ChIP-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. More details of EDDA can be found at Luo, Huaien et al. “The Importance of Study Design for Detecting Differentially Abundant Features in High-Throughput Experiments.” Genome Biology 2014;15(12):527 (http://www.ncbi.nlm.nih.gov/pubmed/25517037/). An accompanying web server (http://edda.gis.a-star.edu.sg/) is available for easy access to some functionality of EDDA. Additionally a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/EDDA.html) is available for easy installation of EDDA R package. -
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Plant Senescence Analysis
Accurate analysis of plant senescence by colour distortion corr
...However, manual inspection is time consuming and its evaluation is subjective. Therefore objective valuation of plant senescence by color image analysis is desirable for high throughput plant phenotyping. The plant colors in images may not represent the original colors of plants due to imperfect camera lenses and camera settings. In this case, color analysis for the senescence estimation may result in significant error. In this method, we propose a novel algorithm to have the effects of both the color distortion correction and the deblurring for senescence analysis. -
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Telomerecat: The Telomere Computatioanl Analysis Tool Telomerecat allows you to generate average TL estimates for any high throughput paired end sequencing samples.
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SALAM
Statistical Analysis of Larval Motions
Automated, high-throughput detection and statistical analysis of behaviors of Drosophila larvae. -
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mCarts
A hidden Markov model to predict clustered RNA motif sites
Many RBPs recognize very short and degenerate sequences, with targeting specificity achieved by mechanisms such as synergistic binding to multiple clustered sites and modulation of site accessibility through different RNA-secondary structures. mCarts integrates the number and spacing of individual motif sites, their accessibility and conservation, which substantially improves signal to noise ratio. This algorithm learns and quantifies rules of these features, taking advantage of a large number of in vivo RBP binding sites obtained from high throughput sequencing of RNAs isolated by cross-linking and immunoprecipitation (HITS-CLIP). We applied this algorithm to study two representative RBPs, Nova and Mbnl. Despite the very low information content in individual motif elements, our algorithm made very specific predictions for successful experimental validation. -
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Net Statistics is a network monitoring tool. Watch device status, parameters and statistics for incoming and outgoing traffic, and summary info. Traffic diagram shows last few minutes in real-time for easy monitoring of network activity.
