Search Results for "genome browser django"
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Showing 49 open source projects for "genome browser django"
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Django Notebook
Django + shell_plus + Jupyter notebooks made easy
Django + shell_plus + Jupyter notebooks made easy. A Jupyter notebook with access to objects from the Django ORM is a powerful tool to introspect data and run ad-hoc queries. Built-in integration with the imported objects from django-extensions shell_plus. Saves the state between sessions so you don't need to remember what you did. Inheritance diagrams on any object, including ORM models. -
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Tactical RMM
A remote monitoring & management tool, built with Django, Vue and Go
Tactical RMM is a remote monitoring & management tool, built with Django and Vue. It uses an agent written in golang and integrates with MeshCentral. Demo database resets every hour. A lot of features are disabled for obvious reasons due to the nature of this app. Teamviewer-like remote desktop control. Real-time remote shell. Remote file browser (download and upload files). Remote command and script execution (batch, powershell and python scripts). -
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Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing... -
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SQL Explorer
Easily share data across your company via SQL queries
SQL Explorer aims to make the flow of data between people fast, simple, and confusion-free. It is a Django-based application that you can add to an existing Django site, or use as a standalone business intelligence tool. Quickly write and share SQL queries in a simple, usable SQL editor, preview the results in the browser, share links, download CSV, JSON, or Excel files (and even expose queries as API endpoints, if desired), and keep the information flowing! -
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Tabby Web
An SSH/Telnet/Serial client in your browser
Tabby Web brings a modern terminal experience to the browser by pairing a web UI with a backend gateway that brokers TCP connections over WebSockets. It aims to deliver an experience similar to the desktop Tabby terminal—sessions, profiles, and rich configuration—while being accessible anywhere through a login. The architecture splits concerns: a Django-based control plane manages users, auth, and configuration, while a gateway service handles network transport so browser clients can reach SSH, Telnet, or serial targets. ... -
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MDN Learning Area
GitHub repo for the MDN Learning Area
learning-area is the official GitHub repository for the MDN Web Docs Learning Area, a collection of educational resources designed to teach core web development technologies. It contains the code examples referenced throughout MDN’s tutorials and articles, covering topics such as HTML, CSS, JavaScript, and web APIs. Each directory in the repository mirrors the module structure of the MDN Learning Area, allowing learners to follow along easily as they read through corresponding lessons. The... -
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GenoViz
Visualization software for genomics
GenoViz provides software applications and re-usable components for data visualization and data sharing in genomics. Our main products are * Integrated Genome Browser (IGB) * GenoViz SDK For more information about IGB, visit https://bioviz.org. Source code for IGB is available from https://bitbucket.org/lorainelab/integrated-genome-browser. For more information about GenoViz SDK, visit https://bitbucket.org/lorainelab/genoviz-sdk. Javadocs for GenoViz SDK are available at https://bioviz.org. ... -
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A... -
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Automation Orchestrator
Automation Orchestrator application to orchestrate digital processes
The Automation Orchestrator allows you to run a local Django Web Application to administrate and orchestrate automation scripts such as Nintex RPA botflows but you may also orchestrate other automation such as Python scripts, batch files, and other RPA tools. The Automation Orchestrator is tested with and supports Nintex RPA version = 15.1. As described on the official Django project site, it "is a high-level Python Web framework that encourages rapid development and clean, pragmatic design. ... -
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workshops_project
Workshops is an open source, simple, dead-lightweight LMS
Workshops is an open source, simple, dead-lightweight LMS (Learning Management System) application programmed in Python (version 3.8.x) with Django (version 2.2.x) web framework which main purpose is to make a standarized way to share knowledge via courses in a slide-based view in browser powered by remark javascript library, easy to create, edit, delete and show your courses using simple markdown and html if necessary. Inspired on an old project in my social labours to help share knowledge in an easy way. -
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Webterminal bastion server
ssh rdp vnc telnet sftp bastion/jump web putty xshell terminal
...Webterminal helper support (use your favorite tools to manage and connect server) VNC, RDP, SFTP Remote file browser (download, delete, update and upload files). Ubuntu webterminal helper support. Mac webterminal helper support. Windows webterminal helper support. Commercial version provides mstsc helper. -
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hiddenDomains
hiddenDomains: a modern HMM to identify ChIP-seq enrichment
hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities. -
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GCB_package
Stand-alone version of the Genome Complexity Browser
This application allows observing genome rearrangements in prokaryotic genomes. It provides rearrangements frequencies profiles and genomes graph representation. -
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PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
PWMScan is used to scan a position weight matrix (PWM) against a genome or, in general, a large set of DNA sequences. The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site. PWMScan takes as... -
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ZENBU is a data integration, data processing, and visualization web system based around three main web interfaces : an expression data enhanced genome browser interface, a secured user system for data upload and secured data sharing, and a data explorer interface to find and manipulate data across the many supported experimental data types and to find shared user configurations ZENBU is built as a web2.0 client/server application with javascript web clients and c++ server infrastructure.
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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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DaMold
a data mining platform for variant annotation and visualization.
...Furthermore, it cross-links each variant with more than 30 clinically relevant public databases, which contain already reported SNPs and INDELs from previous experimental studies along with associated genomic, proteomic, and clinical information. DaMold seamlessly integrates six widely used genome browser such as the UCSC genome browser, Ensembl genome browser, GWAS central genome browser, HapMap genome browser, 1000 Genomes browser, and NCBI variation viewer. Each variant is directly linked with each genome browser. DaMold can be used to analyze, elucidate, and interpret variants from data generated by NGS in clinical research. -
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GNomEx
A Genomic LIMS and Data Repository
...Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing, Affy and Agilent Microarrays, Sequenom MassArray and Bioanalyzer. GNomEx is a web application with a Flash client user interface and a Java backend that runs on Apache Tomcat. ... -
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MSRE-HTPrimer
A high-throughput primer design tool for MSRE-assay in epigenetics
...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 features: 1) visualization of primer pairs in UCSC genome browser, 2) search each resulting primer pair in UCSC In-Silico PCR database, 3) flexible primer selection and filtering based on custom quality matrix and 4) parallel primer design for several target sequences. The pipeline is equipped with multiprocessing capability and uses custom inputs and parameters to design specific primers. -
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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in... -
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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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 and primers can be made to avoid overlapping SNPs for genomes where SNP databases are available. -
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade-defining polymorphism. ... -
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GESPA
Accurately predicts disease association of single nucleotide mutations
GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs are... -
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DeepView
DeepView: RNAseq Viewer
DeepView: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks
