Search Results for "gene"
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Showing 395 open source projects for "gene"
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MCScanX
MCScanX: Multiple Collinearity Scan toolkit X version
MCScanX is a toolkit for detecting gene synteny and collinearity, aiding in the evolutionary analysis of gene arrangements across multiple genomes. It extends the original MCScan algorithm by incorporating additional utilities for visualization and downstream analyses. -
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clusterProfiler
A universal enrichment tool for interpreting omics data
clusterProfiler is an R/Bioconductor package that provides a unified workflow for functional enrichment analysis to interpret high-throughput omics results. It supports both over-representation analysis and gene set enrichment analysis, letting you work with unranked gene lists or ranked statistics from differential pipelines. The package connects to multiple knowledge bases—such as Gene Ontology, KEGG, Reactome, Disease Ontology, MeSH and others—through a consistent interface so you can query different biological lenses without rewriting code. ... -
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gene-archive
Static site generator for a family history archive: interactive tree, person cards, documents, places map, story. RU/EN/RO interface, living people hidden, GEDCOM import/export. Генератор сайта семейного архива.
gene-archive is an MIT-licensed generator for family history websites. It combines an interactive family tree, person cards linked to documentary sources, scans and PDF previews, family narratives and a places map. Data is stored in one JSON file, with GEDCOM import/export and an English, Russian and Romanian interface. Generated static HTML can be hosted without a database. -
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nichenetr
NicheNet: predict active ligand-target links between interacting cells
...NicheNet prioritizes ligands according to their activity (i.e., how well they predict observed changes in gene expression in the receiver cell) and looks for affected targets with high potential to be regulated by these prioritized ligands. -
Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
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Circuitscape.jl
Algorithms from circuit theory to predict connectivity
Circuitscape is an open-source program that uses circuit theory to model connectivity in heterogeneous landscapes. Its most common applications include modeling the movement and gene flow of plants and animals, as well as identifying areas important for connectivity conservation. The new Circuitscape is built entirely in the Julia language, a new programming language for technical computing. Julia is built from the ground up to be fast. As such, this offers a number of advantages over the previous version. -
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RemixIcon
Open source neutral style icon system
Remix Icon is a set of open-source neutral-style system symbols for designers and developers. Unlike a patchwork icon library, 2400+ icons are all elaborately crafted so that they are born with the gene of readability, consistency and perfect pixels. Each icon was designed in "Outlined" and "Filled" styles based on a 24x24 grid. Of course, all the icons are free for both personal and commercial use. Open-source neutral-style system symbols are elaborately crafted for designers and developers. All of the icons are free for both personal and commercial use. -
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Scanpy
Single-cell analysis in Python
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. -
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AlphaGenome
Programmatic access to the AlphaGenome model
...This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can deliver predictions at single-base-pair resolution for most outputs. AlphaGenome achieves state-of-the-art performance across a range of genomic prediction benchmarks, including numerous diverse variant effect prediction tasks. -
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Prokka
Rapid prokaryotic genome annotation
...Because it standardizes names, locus tags, and qualifiers, Prokka is often used as a baseline for comparative microbial genomics, pangenome studies, and functional profiling. Its modular design lets users plug in custom gene callers or databases, making it flexible for diverse research contexts. -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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JuiceFS
JuiceFS is a distributed POSIX file system built on top of Redis
...Whether it's a public cloud, private cloud, or hybrid cloud, JuiceFS is available on any cloud of your choice and delivers flexibility, availability, scalability and strong consistency for your data-intensive applications. Purposely built to serve big data scenarios such as self-driving model training, recommendation engine, and Next-generation Gene Sequencing, JuiceFS specializes in high performance and easier management of tens of billion of files management. We bring JuiceFS to developers with the hope that it will be easy to use, reliable, high-performance, and solve all your file storage problems in a cloud environment. -
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Several packages and classes for LaTeX are hosted here.
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BRGV-OS
Linux distributions based on Void Linux
BRGV-OS is a Linux distribution based on Void Linux, with packages manager xbps. ISO files is in brgv-os directory. The work was do it for our job needs (Gene Bank research institute from Suceava, Romania), but anyone can modify for their needs. The name BRGV mean in Romanian "Banca de Resurse Genetice Vegetale" (shortly in English is Gene Bank), an OS mean of course Operating System. Starting with release 23092026 introduces two distinct hardware profiles: a Generic stable ISO and a highly tailored edition optimized specifically for Slimbook EVO laptops running AMD Strix Point architectures. -
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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. -
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AngClust
AngClust: Angle-based feature clustering for time series
... * The clustering outcome of our algorithm (AngClust) is better than the currently most popular STEM algorithm. * AngClust can be used to analyze any short time series gene expression profiles. -
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FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.
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GeneMiner2 is a comprehensive toolkit designed for phylogenomic genomics. Its main functionalities include: - Mining single-copy nuclear genes, plastid genes/genomes, and other molecular markers from next-generation sequencing data. - Aligning and trimming multiple molecular markers, constructing concatenated and coalescent-based phylogenetic trees, and calibrating tree time. Reference for GeneMiner2: Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y. 2026. GeneMiner2:...
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MPIGeneNet
Parallel tool to construct gene co-expression networks
MPIGeneNet is a parallel tool to construct gene co-expression networks using Pearson’s correlation and Random Matrix Theory (RMT). This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). MPIGeneNet integrates the whole procedure of creating the in one program, which makes the tool easier to work with (the users only have to launch the application once) and avoids writing/reading from intermediate files among the modules. -
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BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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IsoQuant
Transcript discovery and quantification with long RNA reads
...If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon, and intron quantification. If reads are grouped (e.g. according to a cell type), counts are reported according to the provided grouping. The latest IsoQuant version can be downloaded from github.com/ablab/IsoQuant/releases/latest. Full IsoQuant documentation is available at ablab.github.io/IsoQuant. -
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Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.
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MetaEntropy
R package for Virome Mutational Analysis
Estimates Shannon entropy, per gene and per genomic position, associated with non-synonymous mutation frequencies in viral populations, such as wastewater samples. The package uses codon translations for functional insights. Each amino acid can be treated as an individual state, resulting in a 20-state entropy computation, or grouped into one of six physicochemical classes, adding further functional context. -
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vcf2maf
Convert a VCF into a MAF
vcf2maf is a Perl-based tool developed by the Memorial Sloan Kettering Cancer Center to convert Variant Call Format (VCF) files into Mutation Annotation Format (MAF) files. This conversion standardizes variant annotations, facilitating downstream analyses in cancer genomics. -
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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.
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Please, do not hesitate to contact us if you need help. https://sites.google.com/view/hsa23/ Shetti is an automated and user-friendly tool to manipulate protein or gene sequences, GenBank and UniProt raw files, and transform them to human-readable format. The tool is developed to help the experimental biologists, without prior programming skills, to manipulate sequences quickly, easily and precisely. The methods implemented in Shetti are simple and basic commands with friendly user interface. ...
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). ...
