Search Results for "genes" - Page 5
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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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From improving customer experience through seamless sign-on to making MFA as easy as a click of a button – your login box must find the right balance between user convenience, privacy and security.
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PanCGP
PanCGP: Pangenome and Comparative Genome Analysis Pipeline tool
Pan-genome and Comparative Genome analysis Pipeline tool is a high performance parallel computing analysis tool. The aim of developing this high performance and scalable pipeline is to reduce the time cost of calculating the pan-genomes from the given dataset of protein sequences of bacterial strains. The pipeline is able to compute pan-genome analysis from unpublished data-sets as well. Those results are interpreted in the form of pan-genome, core genome/proteins, dispensable genes/proteins... -
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DNA patterns & application
A software for generating DNA patterns
The DNA pattern represents a new method of analysis for DNA sequences. In general it can easily detect relationships among species over the evolutionary landscape. Largely, in bioinformatics the DNA pattern method is unexplored and many discoveries can be made through it. One of the questions to which an answer was given is: How many types of promoters are out there regulating the genes ? It seems that there are 10 types of promoters. The project also contains 20,000 images (DNA patterns... -
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EPIG-Seq
Extracting Patterns and Identifying co-expressed Genes from RNA-Seq
An algorithm and software to identify gene expression patterns from RNA-Seq count data. Once the patterns are identified, co-expressed genes are clustered to the patterns. -
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SAT-Assembler
Scalable and accurate targeted gene assembly for large-scale NGS data
SAT-Assembler is a scalable and accurate gene assembly tool for large-scale RNA-Seq and metagenomic data. It recovers genes from gene families of particular interest to biologists with high coverage, low chimera rate, and extremely low memory usage compared with exiting gene assembly tools. Moreover, it is naturally compatible with parallel computing platforms. -
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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
...), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. We demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. -
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... segmentation. The proposed segmentation procedure yields the spots median intensity values for the microarray images recorded from Cy3 and Cy5 fluorescent dyes. Based on the fold change factor, the differentially expressed genes were determined. Both images with single spot groups and multiple spot groups (372 and 324 spots/group) can be processed. Example of such images were taken from the GEO and SMD databases. e.g., GSM102718 - GEO experiment for single spot group.
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BACNET
An interactive platform for analysis and publication of bacterial omic
... with proteomics and genomics data. This genome viewer is able to load quickly every data using streaming techniques, to zoom through the data from a nucleotide scale to a genome-wide scale, and overlay heterogeneous “omics” data. And an expression atlas, inspired from EBI Expression Atlas, for easily design a query based tool which connects every genomics elements (genes, smallRNAs, antisenseRNAs) to the most relevant “omics” data. -
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FuncEpiMod
Identification of Functional Epigenetic Modules (FEM)
An R-package implementing an algorithm, called FEM, for identifying genes modules of coordinated differential expression and differential methylation associated with a phenotype of interest. The modules are inferred as heavy subgraphs on an interaction network where weights are constructed from the statistics of differential expression and differential methylation. Note: latest version of R-package will be available from Bioconductor (www.bioconductor.org) -
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HardCORE
HardCORE will find the core,pan and accessory genes from genomes
This script will search for all orthologs or core genes that occur between the genomes that are provided as input. In addition the genes that are unique to s single genome will be outputted (accessory) as well as the pan genome (all the genes found amongst genomes). The input must consist of either closed genomes or denovo assembled genome fasta files. -
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BiRW
Bi-random Walks for Phenome-Genome Association Prediction
The availability of ontologies and systematic documentations of phenotypes and their genetic associations has enabled large-scale network-based global analyses of the association between the complete collection of phenotypes (phenome) and genes. BiRW is a package designed for analysis and prediction of the phenome-genome associations. BiRW package contains a program for analysis of circular bigraphs (CBGs) and the bi-random walk (BiRW) algorithm to capture the CBG patterns in the networks... -
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PanCoreGen1
A comprehensive tool to profile, detect & annotate microbial genomes.
PanCoreGen is a Windows-based standalone tool offering 4-in-1 functionalities – (i) pan-/core-genomic profiles across the entire sample set; (ii) similar profiles within user-defined strain-groups; (iii) annotations of user-provided draft genomes; and (iv) detection of unidentified genes in annotated genomes. -
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libtext_bayes
Naive Bayes algorithm text classifier C++ library...
This is a Naive Bayes text classifier library to C++, you can classify SPAM messages, genes, sentiment types in texts. Naive Bayes has been studied extensively since the 1950s. It was introduced under a different name into the text retrieval community in the early 1960s, and remains a popular (baseline) method for text categorization, the problem of judging documents as belonging to one category or the other (such as spam or legitimate, sports or politics, etc.) with word frequencies... -
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BAGEL: analysis of gene knockout screens
BAGEL: Bayesian Analysis of Gene EssentiaLity
BAGEL: software for Bayesian analysis of gene knockout screens using pooled library CRISPR or RNAi. BAGEL is a Bayesian classifier for pooled library genetic perturbation screens, using either CRISPR-Cas9 or shRNA libraries. It uses training sets of known essential and nonessential genes to estimate what the fold change distribution of an essential or nonessential gene should look like. Then, for each uncharacterized gene, it takes all observations of reagents targeting that gene (guide RNA... -
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LowMACA
Low frequency Mutation Analysis via Consensus Alignment
The remarkable efforts recently carried out to fully understand the mutational landscape of various kinds of cancer have revealed that the mutational processes can be extremely variable depending on the tumor type and the clinical features of patients. Thanks to these efforts, we have reached a clear picture of the most commonly mutated genes in various types of cancer. However, we are still far from a complete picture of rarely mutated genes, which can be an important target for personalized... -
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Relative Metabolic Differences
RMetD scripts
The scripts for Relative Metabolic Differences (RMetD) method which is RAVEN compatible and developed in Matlab. This script is mainly used for compare the difference of two cells based on the differentially expressed genes between them and use genome-scale metabolic model as platforms. -
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GOBIG is a toolbox that can be used for detecting genetic variations. The project is intended to handle big data. What's more important is that it be used to detect clusters of SNP variants. It is the intention to use the toolbox with common and rare variants. To use it, for example, to find the genetic map of genes causing complex diseases.
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MESPA is a python based pipeline that builds gene models from fragmented genome assemblies. The identification of genomic regions underlying phenotypic differences is central to many questions in evolutionary biology. These studies involve the generation of a high-quality genome and annotation, which consumes a considerable amount of resources in terms of time, money, and personnel. However, most of the causal variation is found in or near genes, so having good gene models is essential. We...
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CoGA
R package for differential co-expression analysis
... interfaces for network visualization, ranking of genes according to their "importance" in the network, and the standard single gene differential expression analysis. -
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APPRIS
A system for annotating alternative splice isoforms
APPRIS is a pipeline that deploys a range of computational methods to provide value to the annotations of the human genome. APPRIS also selects one of the CDS for each gene as the principal functional isoform. Recent studies have estimated that almost 100% of multi-exon human genes produce differently spliced mRNAs. It is important to designate one of the isoforms as the "principal" functional isoform in order to predict changes in function, structure or localisation brought about... -
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merlin is an user-friendly Java application that performs the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs several steps of the reconstruction process, including the functional genomic annotations of the whole genome. Moreover, merlin includes tools for the identification and annotation of transport proteins encoding genes, as well as the generation of transport reactions for such carriers. Also, merlin includes tools...
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QueTAL-effectors
suite to compare TAL effector sequences
The suite QueTAL was developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effetors with similar DNA-binding capabilities. It calculates correlations between positional weight matrices obtained from the RVD sequence, and builds trees... -
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Transcriptome assembly ORA
Reference-based transcriptome reconstruction software
Sofware for reference-based transcriptome reconstruction. It performs reconstruction starting from short reads obtained from RNA-seq. It is best suited to manage the transcriptomes of lower eukaryotes with a low number of introns per gene and it can be used also for procariotes. It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome. It provides in output the positions of the transcripts identified... -
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Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.
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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... -
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Genome Rearrangements are large-scale mutational events that affect genomes during the evolutionary process. Therefore, these mutations differ from punctual mutations. They can move genes from one place to the other, change the orientation of some genes, or even change the number of chromosomes. In this work, we deal with inversion events, which occur when a segment of DNA sequence in the genome is reversed. In our model, each inversion costs the number of elements in the reversed segment. We...