Search Results for "genes" - Page 4
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Showing 268 open source projects for "genes"
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SKUDONET ADC, operates at the application layer, efficiently distributing network load and application load across multiple servers. This not only enhances the performance of your application but also ensures that your web servers can handle more traffic seamlessly.
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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HPOSim
Analysis phenotypic similarity between genes and between diseases
This package implements multiple similarity measures for HPO terms, genes and diseases. It is aiming at phenotype analysis for gene sets and disease sets. Functions for HPO enrichment analysis is also provided. -
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This software is intended to identify the differentially expressed genes from the given set of genes. The data is input by the user in the form of Comma Delimited (.csv) Microsoft Excel (2007 and above) File.
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Crosshub
Multi-way analysis of The Cancer Genome Atlas (TCGA) project datasets
Crosshub enables multi-way analysis of RNA-Seq, miRNA-Seq and methylome data of The Cancer Genome Atlas (TCGA) project: 1. differential expression analysis (genes, alternative transcripts and miRNA) 2. regulatory miRNA prediction (TargetScan, DIANA microT, mirSVR, PicTar, miRTarBase + co-expression) 3. regulatory TF prediction (ENCODE ChIP-Seq + co-expression) 4. methylation profiling analysis 5. RNA-Seq vs. clinical (TNM, stage, follow-up) correlation analysis Generates Excel summaries... -
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HGPEC
A tool for gene and phenotype prioritization and evidence collection
Finding gene-disease and disease-disease associations are important issues in the biomedical area and many prioritization methods have been proposed for this goal. Among these, approaches based on heterogeneous network of genes and phenotypes were considered state-of-the-art ones, which can use for diseases with/without known molecular basis. Here, we develop a Cytoscape plugin, namely HGPEC, based on a ran-dom walk with restart algorithm on a heterogeneous network of genes and phenotypes... -
Over two-thirds of people reuse passwords across sites, resulting in an increasingly insecure e-commerce ecosystem. Learn how passwordless can not only mitigate these issues but make the authentication experience delightful. Implement Auth0 in any application in just five minutes
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GetX
An automated mutation cassette design tool for scarless genome editing
..., insertions, and point mutations. It also designs synonymous codon fragments required to manipulate essential target genes to enable survival of the strain during the genome editing procedure. GetX provides genbank and fasta format files for a mutation template plasmid, a mutation cassette, and a sequence around the mutation site to guide the user through the design of the materials required for the scarless bacterial genome editing method. -
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ConsPred
ConsPred is a pipeline combining several gene/CDS annotation tools
ConsPred is a prokaryotic genome annotation framework that performs various intrinsic gene predictions, homology searches, predictions of non-coding genes, and complex features and integrates all evidence into a consensus annotation. ConsPred achieves high-quality and comprehensive annotations based on rules and priorities, similar to decision making in manual curation. Parameters controlling the annotation process are configurable by the user and the framework can be easily extended... -
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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... -
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TAL evolution scripts
Scripts to assess TAL effector diversity and find evolutionary pattern
TAL effectors (aka TALEs) are repeat containing proteins found in the genus of phytopathogenic bacteria Xanthomonas. They are able to bind DNA through their repeat region and induce genes in the host plant. Thus variation in repeat number and order can lead to diversification of virulence functions and evasion of recognition by the host. Variation in TAL effector repeats and repeat sequence between different taxonomic groups has remained largely unexplored. In this study we describe... -
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ETHA
Hybrid Illumina/PacBio assembly of Plasmodium falciparum var genes
ETHA is a software package for hybrid assembly of Plasmodium falciparum var genes from Illumina and PacBio sequencing data -
ConnectWise ScreenConnect, formerly ConnectWise Control, is a remote support solution for Managed Service Providers (MSP), Value Added Resellers (VAR), internal IT teams, and managed security providers. Fast, reliable, secure, and simple to use, ConnectWise ScreenConnect helps businesses solve their customers' issues faster from any location. The platform features remote support, remote access, remote meeting, customization, and integrations with leading business tools.
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Survive
A survival game with zombies.
This is a zombie survival game that takes place in a post-apocalyptic atmosphere. It takes place right after a failed attempt to cure cancer caused the genes inside of all human bodies to become brain-dead zombies. Shoot zombies, eat to live, and survive the horde! -
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Integrated Merging of Orthogonal [Genetic] Datasets to identify novel genes involved in processes starting with known genes. For UNIX-like systems (C code + TCSH scripts), command-line based.
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Analyze My Genes
Compare gene analysis results from 23andme with the human genome
This program compares personal gene analysis results from 23andme with extracted databases from the human genome project. An typical example of an extracted database is a dataset which contains all alternative alleles which occur less than 1% of the time. -
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metawatt
Binner for assembled metagenomes
The Metawatt binner is a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning. It also performs taxonomic assessment of binning quality (via diamond BLASTx). Created bins can be edited and exported as fasta. The Metawatt is implemented in Java SWING and minimally depends on Diamond, HMMer3.1, BBMap, Prodigal and the Batik library for the export of SVG graphics. Citation: Strous M, Kraft B, Bisdorf R,... -
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... be used for downstream analysis including assembly to identify genes that are differentially abundant between groups of metagenomes (e.g., healthy vs diseased). Please refer to our RECOMB paper for more details: Wontack Han, Mingjie Wang and Yuzhen Ye. A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes. Proceeding of RECOMB 2017.
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result... -
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PExFInS
Post-GWAS Explorer for Functional Indels and SNPs
The generation of Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) was originated from the observation that high proportion of cis-acting expression quantiative trait loci (cis-eQTLs) emerged in GWAS SNPs and the underexplored status of indel cis-eQTLs for GWAS. We believe that the integration of cis-eQTLs, especially indel cis-eQTLs, with candidate disease-associated variants generated from GWAS could facilitate the identification of causal genes or disease mechanisms. On the other... -
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WIMSi
Bioinformatics Tools for the Anaysis of DNA Methylation Data
... about what patterns should exist in the data. The GENE LIST tool is designed to take advantage of the patterns found to elucidate genes likely regulated by DNA methylation. -
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The objective of this project is to provide an innovative tool for visualization of multiples genomes. Written in Java, it presents a simple and intuitive user interface to view and manipulate the relationships between groups of genes.
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A program that finds and annotates genes using contigs and singletons yielded from microarray assays.
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CoNet
Find relationships between repeatedly observed items
CoNet is a Cytoscape plugin that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. It has been designed with (microbial) ecological data in mind, but can be applied in general to infer relationships between objects observed in different samples (for example between genes present or absent across organisms). -
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goSTAG
Gene Ontology Subtrees to Tag and Annotate Genes within a set
We developed goSTAG for utilizing Gene Ontology Subtrees to Tag and Annotate Genes that are part of a set. Given gene lists, goSTAG performs GO enrichment analysis and clusters the GO terms based on the p-values from the significance tests. GO subtrees are constructed for each cluster, and the term that has the most paths to the root within the subtree is used to tag and annotate the cluster. -
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PGAP
PGAP is a pipeline for pan-genome analysis.
PGAP is a pan-genomes analysis pipeline developed with Perl. It could perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. -
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Unravel motifs in UTRs and introns
Unravel motifs in UTRs and introns
What are the sequence logos for the regions before and after the translation start site? the beginning and end of the first intron (for those genes that have at least one intron)? Note that this project involves gathering the data and preparing it, which in this case involves (at least) to align sequences before trying to get a sequence logo. -
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Protein Expression Control Analysis (PECA) is a statistical software to identify genes subject to significant RNA- and protein-level regulation with control of false discovery rate.
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Re-Annotator
Re-annotates Microarray Probes
The microarray technology is an established approach for high throughput gene expression analysis. An accurate mapping between array probes and the genes that they are targeting is essential for generating accurate biological findings. The manufacturers typically provide such annotation tables. However, these tables rely on older genome and transcriptome versions that differ substantially from the current state-of-the-art sequence databases. Re-Annotator is a re-annotation pipeline for gene...