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Showing 9 open source projects for "gene code"

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1

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. ...

Downloads: 8 This Week

Last Update: 4 days ago
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2

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/

Downloads: 1 This Week

Last Update: 2025-04-11
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3

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 Please note: 1) The SourceForge version of COHCAP is no longer being updated.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...

Downloads: 1 This Week

Last Update: 2023-06-13
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4

Jenetics: Java Genetic Algorithm Library

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.

8 Reviews

Downloads: 0 This Week

Last Update: 2018-11-10
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5

INTEGRATE

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.

Downloads: 0 This Week

Last Update: 2016-11-29
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6

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)

Downloads: 0 This Week

Last Update: 2016-02-23
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7

GenoCAD

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.

Downloads: 5 This Week

Last Update: 2015-04-19
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8

GMDR

A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

2 Reviews

Downloads: 1 This Week

Last Update: 2016-03-13
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9

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.

Downloads: 0 This Week

Last Update: 2019-03-07
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