Search Results for "dna"
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Showing 445 open source projects for "dna"
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Discourse Network Analyzer (DNA)
Discourse Network Analyzer (DNA)
The Java software Discourse Network Analyzer (DNA) is a qualitative content analysis tool with network export facilities. You import text files and annotate statements that persons or organizations make, and the program will return network matrices of actors connected by shared concepts. -
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pydna
Clone with Python! Data structures for double stranded DNA
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning. Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways, are often difficult to properly document as is evident from the poor state of documentation in the scientific literature. The pydna python package provide a human-readable formal description of cloning and genetic assembly strategies in Python which allow for simulation and verification. ... -
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Evo 2
Genome modeling and design across all domains of life
Evo 2 is a DNA language model system designed for long-context genome modeling and biological sequence design across all domains of life. The project models DNA at single-nucleotide resolution and supports context windows of up to one million base pairs, which places it in a class of models built for very large genomic reasoning tasks. According to the repository, it uses the StripedHyena 2 architecture, was pretrained with Savanna, and was trained autoregressively on the OpenGenome2 dataset containing 8.8 trillion tokens. ... -
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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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Marin
Framework for research and development of foundation models
...Experiments and decisions are documented as they occur, including unsuccessful approaches. The framework is primarily used for large language models but has also supported audio-text, DNA, and protein modeling research. Experiments are expressed as dependent steps that execute in topological order, enabling reproducible training workflows. Marin also provides model checkpoints, training recipes, scaling research, documentation, and reusable infrastructure for large-scale experiments. -
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ESPResSo
The ESPResSo package
...It is designed for coarse-grained and bead-spring models used in physics, chemistry, and molecular biology. The software can model systems such as polymers, colloids, liquid crystals, ferrofluids, DNA, lipid membranes, and other complex fluids. It includes a broad range of interaction potentials and algorithms for electrostatics, hydrodynamics, and coupled particle-field behavior. ESPResSo is controlled through Python, which makes it flexible for custom simulation setup and analysis. Its main value is giving soft matter researchers a versatile and extensible platform for studying many-particle systems beyond simple atomistic models. -
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nuwa-skill
Mental models, decision heuristics, expressing DNA
nuwa-skill is an AI-oriented project focused on defining, managing, and executing modular “skills” that can be used by intelligent agents or automation systems. It provides a framework for organizing capabilities into reusable units that can be invoked dynamically depending on context or user input. The project is designed to integrate with AI systems, enabling them to perform structured tasks such as data retrieval, processing, or interaction with external services. It emphasizes modularity... -
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DeepVariant
DeepVariant is an analysis pipeline that uses a deep neural networks
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. DeepTrio is a deep learning-based trio variant caller built on top of DeepVariant. ... -
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AWS ParallelCluster Cookbook
The Chef cookbook used to build and bootstrap AWS ParallelCluster
...AWS ParallelCluster facilitates both quick start proof of concepts (POCs) and production deployments. You can build higher-level workflows, such as a Genomics portal that automates the entire DNA sequencing workflow, on top of AWS ParallelCluster. Node.js is required by AWS CDK library used by ParallelCluster. -
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Bowtie 2
A fast and sensitive gapped read aligner
...Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. Overall, Bowtie 2 remains a foundational command-line tool for high-throughput sequence alignment and reproducible computational biology workflows. -
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AWS ParallelCluster Node
Python package installed on the Amazon EC2 instances
...AWS ParallelCluster facilitates both quick start proof of concepts (POCs) and production deployments. You can build higher-level workflows, such as a Genomics portal that automates the entire DNA sequencing workflow, on top of AWS ParallelCluster. -
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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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binocular
Binocular segmentation of whole-genome DNA sequence data
Segmentation-based detection of copy-number alterations and allelic imbalances in whole-genome DNA sequence data. -
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# Verbium™ - DNA Edition 💎 **Verbium™** is a secure, high-performance binary text editor designed for privacy, integrity, and extreme document handling. Featuring the advanced **DNA Binary Format (v1.4)** and a Minecraft-inspired virtualization engine, Verbium™ can handle near-infinite documents with ease.
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proSeq
ProSeq is a GUI program to edit and analyse DNA polymorphism datasets
ProSeq ('Processor of sequences') is a package including GUI and command line programs to process and analyse DNA polymorphism data. It allows one to open and save sequence data in over a dozen file formats (and convert between these formats). It shows sequence alignments in a graphical window and allows the user to edit, manipulate and analyse sequences in various ways. ProSeq4 includes tools to analyse DNA polymorphism, scan for selection, do PCA and reconstruct phylogenies from sequence or SNP data. ... -
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oxDNA
A code primarily aimed at DNA and RNA coarse-grained simulations
The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases. -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs. Online webserver https://shinywgcna.serve.scilifelab.se/app/shinywgcna PLEASE NOTE Datasets with larger dimensions (e.g., 1000x100) may fail on the server,because it is only running on 1GB RAM allocation. ...
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dnaSPiDER
dnaspider.exe - Programmable keyboard software for Windows
Custom keyboard shortcuts. Simulate keyboard, mouse https://github.com/dnaspider/dna/releases/tag/v1.0.0.189 -
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hg38 version of the pipelines for whole exome sequencing: exome_test38.sh wole transcription sequencing: rna_test38.sh somatic calling: somatic38.sh SV detect: svdetect38.sh, meerkat38.sh cnv: svdetectcnv38.sh, contra38.sh, cnvkit38.sh *** Mutect2 instead of haptotypecaller is used to call variants in DNA-seq.
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UniversalMer2
A CLI k-mer counting tool for multiple size of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). This kmax can be specified as any length or can be automatically determined by the longest repeated patterns found in the input sequence. -
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BBMap
BBMap short read aligner, and other bioinformatic tools.
...It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. ... -
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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MEDe-KIT
Micro Educational and Development Kit (MEDe-KIT)
Micro Educational and Development Kit (MEDe-KIT) is an educational software for storing and viewing information about study material information uploaded to it like images and text descriptions. It uses ODBC for storing uploaded data into local database. Its features also include a genes sequencer for generating combination of DNA and RNA sequence entered. Thanks and hope this is useful for everyone who are interested in science and learning. The project was developed using NetBeans IDE and Java. Default login user name : user Default login password : user
