Search Results for "gene code"
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Showing 25 open source projects for "gene code"
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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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AlphaGenome
Programmatic access to the AlphaGenome model
The AlphaGenome API provides access to AlphaGenome, Google DeepMind’s unifying model for deciphering the regulatory code within DNA sequences. 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. ... -
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CStone
Short-read de novo assembler that identifies chimeric contigs.
> CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through... -
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gcdm
Gene Circuit Dynamical Model
This program implements gene circuit dynamical model of segmentation genes in Drosophila embryo. The code was originally based on the code FlyCode: http://flyex.uchicago.edu/newlab/download/fly9.4_ser.tar.gz -
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hbyao-GIW2019
Materials for problem and optimization of CARD
...We reveal some problematic cases where possible false classifications may occur and methods to solve the problem are proposed. Our paper "Deep Analysis and Optimization of CARD Antibiotic Resistance Gene Discovery Models" will be presented on GIW2019. The repository contains the full powerpoint and the code used in our paper. The code and more instructions for using the code will be continuously updated. We look forward to producing a functional plug-in to the CARD database. We sincerely appreciate if you can follow the progress of this project. ... -
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The source code has been migrated and is now hosted on Github: https://github.com/jenetics/jenetics Jenetics is an advanced Genetic Algorithm, Evolutionary Algorithm and Genetic Programming library, respectively, written in modern day Java. It is designed with a clear separation of the several algorithm concepts, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function.
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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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INTEGRATE: Calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. To download source code, reference manual and test case, please go to 'Files'. Also refer to 'Wiki' for details.
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...Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. HeatmapGenerator is released under the GNU GPL.
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scell
single-cell RNA-seq analysis software
SCell is an integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large ensembles of single-cell RNA-seq datasets. SCell is open source, and implemented with an intuitive graphical interface. Binary executables for Windows, MacOS and Linux are available at http://sourceforge.net/projects/scell, source code and pre-processing scripts are available from https://github.com/diazlab/SCell. ... -
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PromKappa 2.0 (DNA patterns in Java)
PromKappa 2.0 (Java source code and bin)
A Java adaptation of DNA patterns based on the article "Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters". by Ilie Guta (Java source code for DNA patterns) -
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DNA patterns & application
A software for generating DNA patterns
...The project also contains 20,000 images (DNA patterns) that can be analyzed in relation to various genetic disorders (if Homo Sapiens) or for understanding the evolutionary mechanisms between species. References: [1] Gagniuc and Ionescu-Tirgoviste: Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics 2012, 13:512. [2] Gagniuc and Ionescu-Tîrgoviste. Gene promoters show chromosome specificity and reveal chromosome territories in humans, BMC Genomics 2013, 14:278. Source code VB6 (Visual Basic 6.0) -
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BiRW
Bi-random Walks for Phenome-Genome Association Prediction
...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 for unveiling human and mouse phenome-genome association. The processed OMIM human disease phenotype-gene association network and MGI mouse phentoype-gene association network are also released together with the source code. -
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Genetic Algorithms Engine - Blackjack
A genetic algortihm engine that evolves blackjack basic strategy.
...To see it in action, download the zip file and run either: GABlackjack_Demo.exe (quick) or GABlackjack_Long.exe (slow, but it achieves better results). The code was written in C++, using MS Visual Studio 6.0 and MS Visual Source Safe 6.0. The genetic algorithm engine supports various mutation rates, ranked parental selection, stochastic sampling parental selection, cyclic crossover, crossover at each gene, cloning the best individual each generation, and creating random individuals each generation. ... -
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simulate_pcr
PCR target prediction software
...This script predicts potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch tolerance and amplicon length range to be set by the user. The PCR amplicon simulation code also annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons. It is an open source command line Perl script called simulate_PCR.pl that calls the BLAST (Altschul, et al., 1990) programs makeblastdb, blastn, and blastdbcmd, and the NCBI efetch utility (http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi). -
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CollapseFPKM
This code is a solution to collapsing duplicate FPKMs for a gene
This code is a solution to collapsing duplicate FPKMs for a gene. Problem/Issue: In the cufflinks output files *_genes.expr (which reports the gene-level coordinates and expression values), sometimes I get more than one row for the same gene? It's like in some cases the FPKM values from the transcripts corresponding to the same gene do not get summed, although the transcripts are assigned to the same gene. -
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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Code for Semi-Supervised Machine Learning Techniques, Self-Learning and Co-training used in the paper: Rania Ibrahim, Noha A. Yousri, Mohamed A. Ismail and Nagwa M, El-Makky. “miRNA and Gene Expression based Cancer Classification using Self-Learning and Co-Training Approaches”. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 495-498, 2013. --------------------------------------------------------------------------- For Self-Learning: java -jar -Xms1700m SelfLearner.jar [trainFile] [testFile] [labelFile] [unlabeledFile] [Alpha] [ClassifierType(randomforest,svm)] [resultFile] [ClassifierModelFile] For Co-Training: java -jar -Xms2500m CoTraining.jar [trainFile-Side1] [testFile-Side1] [labelFile-Side1] [unlabeledFile-Side1] [trainFile-Side2] [testFile-Side2] [labelFile-Side2] [unlabeledFile-Side2] [MappingFile] [Alpha] [ClassifierType(randomforest,svm)] [resultFile] [ClassifierModelFileSide1] [ClassifierModelFileSide2]
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A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions
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This is C++ application code that implements Gene Expression Programming, or GEP - a form of genetic algorithm.
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SEO Tools provides tools for search engine optimization. Spider SEO: generates meta tags for all pages of a website. Web Page Optimizer performs analysis and changes in a web page. A graphical user interface is linked with a scriptol program that gene
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Autoprime
Automated primer design using EnsEMBL
AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression. By connecting to the EnsEMBL database gene structure information is used to find primers spanning exon borders. This way only expressed sequences are captured. Additionally mispriming on repetitive regions can be avoided using information from RepBase. -
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V4ALL Eclipse GUI Designer An Eclipse Plugin for Designing Java Swing & SWT GUI´s and generating the code. The design model has XML format ans is rather abstract and not tidely coupled with the generated target API. So with V4ALL and additional gene
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