Search Results for "gene"
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Showing 487 open source projects for "gene"
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Several packages and classes for LaTeX are hosted here.
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nichenetr
NicheNet: predict active ligand-target links between interacting cells
nichenetr: the R implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. This model of prior information on potential... -
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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... -
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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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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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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... -
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JuiceFS
JuiceFS is a distributed POSIX file system built on top of Redis
..., 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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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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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction... -
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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... -
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... as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. The user is able to change the main parameters of the analysis in the graphical interface.
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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. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
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BD-Func
Bidirectional Functional Enrichment of Gene Expression Data
BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159 -
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Mutation2 Rust
Program to show point mutation, insertion and deletion on DNA, RNA
You can watch the result of point mutation, insertion and deletion on a short strand of DNA, the complementary strand of RNA and the Amino Acids -
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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...
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Shetti can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. 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...
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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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CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics... -
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Cylindrical Alignment App
Arranges alignments in a rotating cylinder
The Cylindrical Alignment App is the successor to Cylindrical BLAST Viewer. Similarly, it arranges search or other comparisons, against their "axis". Searches can be made by Basic Local Alignment Search Tool, ClustalW, or Gene Machine to name a few. This version does not require downloading or installing Java3D, and has more modern GUI features. -
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MaChIAto Example Files
The example files of MaChIAto
MaChIAto (Microhomology-associated Chromosomal Integration/editing Analysis tools); a comprehensive analysis software that can precisely classify, deeply analyze, correctly align, and thoroughly review the targeted amplicon sequencing analysis data obtained by various CRISPR experiments, including template-free gene knock-out, short homology-based gene knock-in, and even a new-class CRISPR methodology, Prime Editing. In this repository, we provide the example files of MaChIAto. You can use... -
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Fusion Detection Pipeline
Fusion gene detection pipeline bundled into a Singularity container.
Fusion gene detection by RNA-seq requires prior setup of several software modules and dependencies which might be troublesome. Furthermore, fusion detection tools tend to report many false positives. Therefore, we developed a detection and filtering workflow bundled into a Singularity container for a streamlined and easy-to-use application. Arriba and FusionCatcher are utilized for fusion calling. Our filtering pipeline uses read counts generated by FeatureCounts and insert size estimation... -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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The Interactome-Transcriptome Integration (ITI) algorithm allows the analysis of gene expression data by superimposition of a large scale protein-protein interaction data (human interactome) over several gene expression datasets. ITI extracts regions in the interactome with differentiating expression over two conditions. These subnetworks can that be used to build a generalizable and stable genomic signature for genomic/cancer classification.
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est-sfs
Estimate the unfolded site frequency spectrum and ancestral states
est-sfs implements a maximum likelihood method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities for DNA sequence data. The uSFS is a vector of counts of nucleotide sites with x derived allele copies in a sample of gene copies from a population. est-sfs infers the uSFS and ancestral state probabilities at polymorphic sites in a focal species using information from up to three outgroup species. Three models of nucleotide substitution have been implemented... -
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SysBioTK
A protein database management toolkit
SysBioTK is a framework which aims to aid in the management of information on proteins from several databases, storing the information in a library. Several search functions are also included in order to filter the proteins in the library. Support for different screenings, such as control groups, is also included. The tool also allows to extract the GeneOntology of the protein/gene list and is able to perform several statiscal tests on the data. This is a renamed and improved version...