Search Results for "novel"
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Showing 19 open source projects for "novel"
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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.
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NeuralOperators.jl
DeepONets, Neural Operators, Physics-Informed Neural Ops in Julia
Neural operator is a novel deep learning architecture. It learns an operator, which is a mapping between infinite-dimensional function spaces. It can be used to resolve partial differential equations (PDE). Instead of solving by finite element method, a PDE problem can be resolved by training a neural network to learn an operator mapping from infinite-dimensional space (u, t) to infinite-dimensional space f(u, t). Neural operator learns a continuous function between two continuous function... -
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awesome-single-cell
Community-curated list of software packages and data resources
... the statistical challenges of single cell RNA-seq. The package incorporates novel and established methods to provide a flexible framework to perform filtering, quality control, normalization, dimension reduction, clustering, differential expression and a wide-range of plotting. An analytical framework for big-scale single cell data. Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction. -
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Koop
Transform, query, and download geospatial data on the web
... including vector-tile, WMS, and plain old GeoJSON. Koop's plugin-architecture facilitates custom deployments specific to your needs. "Provider" plugins to connect to novel data formats and translate to a common format (GeoJSON), while "output" plugins then transform that GeoJSON to other specifications. See a list of plugins already authored and maintained here. If you have a novel data source or require an as-yet unsupported output format, new plugins can be easily developed and integrated. -
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ggforce
Accelerating ggplot2
ggforce is an extension package for ggplot2 that introduces specialized statistical transforms, geoms, and layout utilities to enhance and complement the built-in ggplot2 offerings. It enables more advanced visualization techniques such as faceting enhancements, hulls, annotation marks, and novel layouts for network data and marked regions. -
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Apache Doris
MPP-based interactive SQL data warehousing for reporting and analysis
Apache Doris is a modern MPP analytical database product. It can provide sub-second queries and efficient real-time data analysis. With it's distributed architecture, up to 10PB level datasets will be well supported and easy to operate. Apache Doris can meet various data analysis demands, including history data reports, real-time data analysis, interactive data analysis, and exploratory data analysis. Make your data analysis easier! Support standard SQL language, compatible with MySQL... -
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scArches
Reference mapping for single-cell genomics
Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data. scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations. -
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SandDance
Visually explore, understand, and present your data
... context as you interact with your data. This new version of SandDance has been rebuilt from scratch with the goal of being modular, extensible, and embeddable into your custom applications. We are open and driven by the community through contributions, feature requests, and discussion. SandDance was created by the Microsoft Research VIDA Group which explores novel technologies for visualization and immersive data analytics. -
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OME-3DR
3D cell reconstruction and quantitative analysis based on OME data
For big OME data analysis, we integrate commonly used quantitative methods, describe our novel strategies to quantify and analyze biological markers related to the cell or organelle spatial-coordinate model, and present open-source OME-3-Dimensional Reconstruction (OME-3DR), a flexible, programmable and batch-oriented tool based on OME data, for reconstructing 3-dimensional (3D) spatial conformations and conducting further analyses, such as the identification, counting, localization... -
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GlycoPAT
Comprehensive, open-source tool for glycoproteomics MS data analysis
GlycoPAT is a modular, open-source MATLAB based toolbox for shotgun mass spectrometry based glycoproteomics data analysis. This program provides a novel platform for the streamlined analysis of traditional LC-MSn based high-throughput experimental data for the identification of site-specific N- and O-linked glycosylation on various proteins. More details are available at https://www.VirtualGlycome.org/glycopat Source code also available at https://github.com/kaichengub/GlycoPAT If you... -
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Random Bits Forest
RBF: a Strong Classifier/Regressor for Big Data
We present a classification and regression algorithm called Random Bits Forest (RBF). RBF integrates neural network (for depth), boosting (for wideness) and random forest (for accuracy). It first generates and selects ~10,000 small three-layer threshold random neural networks as basis by gradient boosting scheme. These binary basis are then feed into a modified random forest algorithm to obtain predictions. In conclusion, RBF is a novel framework that performs strongly especially on data... -
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SmartRoot
Semi-automated root image analysis software
... to specific research requirements. SmartRoot is an operating system independent freeware based on ImageJ and uses cross-platform standards (XML, SQL, Java) for communication with data analysis softwares. To cite us: Guillaume Lobet, Loïc Pagès and Xavier Draye. A Novel Image Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture. 2011 Plant Physiology, Vol. 157 -
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chipexo
model based analysis of ChIP-exo data
Here we developed a novel analysis framework named MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. MACExo has the following four steps: 1) sequencing data normalization and bias correction; 2) signal consolidation and noise reduction; 3) single nucleotide resolution border detection using Chebyshev Inequality; and 4) border matching using Gale-Shapley’s stable matching algorithm. When applied to yeast Reb1 and human CTCF ChIP-exo data, MACE is able to define TFBSs... -
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular... -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
... the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. Recently, the advent of next generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf files as an input file, our program identifies the majo -
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BriPy
A BRIC-seq data analysis package written in Python.
-What is BRIC-seq? BRIC-seq, short for 5'-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis, is a novel method in Next Generation Sequencing (NGS) to determine the RNA stability of each transcript. It employs metabolic labeling by BrU of newly synthesized RNAs to chase chronological decreases of BrU-labeled RNA (Pulse-chase labeling), followed by immunoprecipitation with antibody for BrU, construction of cRNA library for High-throughput sequencing and computational data... -
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MolBioLib
C++11 framework for rapid develop and deploy of bioinformatic tasks.
..., ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. While MolBioLib was designed primarily for bioinformatics purposes, much of its functionality is applicable to a wide range of problems. Complete documentation and an extensive automated test suite are provided. This package assumes fluency in both UNIX and C++. -
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VISPA is a novel development environment for high energy physics analyses, based on a combination of graphical and textual steering. The main goal of VISPA is to support users in prototyping, performing, and verifying a data analysis of any complexity.
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Java package to study a clustering model described in the paper \"Novel Clustering Algorithm Based Upon Games on Evolving Network\" by Q. Li, Z. Chen, Y. He and J-P. Jiang (in arxiv: http://arxiv.org/pdf/0812.5064v1), generalizations and similar issues.
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DiscriAlign implements a novel algorithm that aligns a set of biological interaction networks.It identifies both functionally conserved and dissimilar regions.
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