Search Results for "package installer linux"
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Showing 112 open source projects for "package installer linux"
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Full-stack observability with actually useful AI | Grafana CloudBuilt on open standards like Prometheus and OpenTelemetry, Grafana Cloud includes Kubernetes Monitoring, Application Observability, Incident Response, plus the AI-powered Grafana Assistant. Get started with our generous free tier today.
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code"... -
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A software package that implements the probabilistic record linkage technique (PRL). This is a new, improved, open-source, multi-platform version of the previously available program, by the same authors.
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Croizat
A software package for quantitative analysis in Panbiogeography
Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach. -
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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ProStack
ProStack - a platform for image processing and analysis
ProStack - a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio -
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal... -
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MicroRNAs (miRNAs) are of significance in tuning and buffering gene expression. Despite abundant analysis tools have been developed in the last two decades, plant miRNA identification from next-generation sequencing (NGS) data remains challenging. Here present a user-friendly pure Java-based software package, SRICATs, which enable researchers to perform all steps of plant miRNA analysis based on convolutional neural network methods. SRICATs outperforms currently popular software tools on the...
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The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters...
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Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR....
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TASSEL
TASSEL is a bioinformatics software package
TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics. -
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coronavirus
The coronavirus dataset
The coronavirus package gives a tidy format dataset of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemic. Relevant and updated information about the virus, such as summary of new cases by country and total number of cases by region can be retrieved from this package. The raw data is pulled and arranged by the Johns Hopkins University Center for Systems Science and Engineering, which is gathered from various leading sources including the World Health Organization, China CDC, US CDC,... -
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GFtbox is a Matlab package for simulating biological growth of leaves, petals, and similar organs.
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BrukerEyes
BrukerEyes is an open-source package for Bruker datasets management
BrukerEyes is a cross-platform open-source package for Bruker datasets management. It helps scientists to explore their datasets easily. This project was supported by: European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 813120 (INSPiRE-MED) © Institute of Scientific Instruments of the Czech Academy of Sciences. -
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viRome
R code/package for virus small RNA sequence data
Please use code here: https://github.com/mw55309/viRome_legacy -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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miRDiana
MATLAB package to find the miRNAs targeting a list of genes
To select miRNA target genes we developed software in MATLAB® (MathWorks®) called miRDiana that collects the union of mouse validated targets from the TargetScan, MicroCosm, mirTarBase and miRWalk 2.0 databases. Firstly, the software downloads each database and preprocesses by standardizing the miRNA and gene names. It strips the miRNA names from the species ids and converts the gene names to the official symbols of the National Center for Biotechnology Information (NCBI) database. Next, for... -
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Antimony
Antimony is a human-readable, human-writable model definition language
Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats. -
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MoPAC
The Modular Pipeline for the Analysis of CRISPR screens
To facilitate the comparison of gene essentialities in two or more cell samples, we propose MoPAC (Modular Pipeline for Analysis of CRISPR screens), a Shiny-driven interactive tool for differential essentiality analysis in CRISPR/Cas9 screens. For installation and usage instructions please refer to the wiki page. -
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DrawGlycan-SNFG
Renders glycans and glycopeptides with frag. info using SNFG format
...Program source code is also provided.. The web and GUI apps do not require any additional software to run. To install the GUI version, simply download and run the installer for PC or Mac. To install in Linux, follow in-package instructions or visit the VirtualGlycome.org FAQ page. The source code can be edited and run using MATLAB2014b or later. How to Cite: DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information Kai Cheng; Yusen Zhou; Sriram Neelamegham Glycobiology (2017) 27 (3): 200-205 Source code also available at: https://github.com/neel-lab/DrawGlycan-SNFGv2 Abstract & Full Text: https://doi.org/10.1093/glycob/cww115 -
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NanoR
R package built to analyze and compare Nanopore data
NanoR is a package for the statistical language and environment R, tested on Unix, MacOSX and Windows, that allows user-friendly analysis and comparison of 1D MinION and GridION X5 sequencing data within acceptable time frames. -
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
This repository contains the most updated code version of MANTIS, the Multi-locus ANTIgenic Simulator R-package. MANTIS is developed and maintained by the Evolutionary Ecology of Infectious Disease (EEID) research group at the Department of Zoology, University of Oxford, UK. For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN... -
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REHUNT
REHUNT (Restriction Enzymes HUNTing)
REHUNT (Restriction Enzymes HUNTing) is a free and open source package implemented in JAVA for providing many useful methods for biological sequence analysis (especially in SNP genotyping) around restriction enzymes. All academic researchers are encouraged to use REHUNT in their studies or to integrate it into their systems and applications. Non-academic users or commercial needs are also welcome to use it. For further information or additional applications, please contact the author... -
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CuiTools (Coo-e Tools) is a freely available package of Perl programs for unsupervised and supervised word sense disambiguation experiments. The name CuiTools comes from the Concept Unique Identifiers (CUIs) found in the Unified Medical Language System.
