Search Results for "dna"
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Showing 301 open source projects for "dna"
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Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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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... -
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SCIPIO ERP
eCommerce framework for multinational omnichannel installations
High-performance DNA for your custom ONLINE SHOP. A flexible composable commerce framework for international and complex multichannel webshops! Scipio ERP is a perfect fit for large-scale, multinational, multichannel operations. Our modern eCommerce store is optimized for a quick time-to-market. You can run multiple at the same time. Highly configurable products and prices, custom promotions and region-based offerings – the store can handle it all. Our web store is mobile-friendly and full... -
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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... -
Build Securely on Azure with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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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. DeepTrio... -
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AWS ParallelCluster Node
Python package installed on the Amazon EC2 instances
... and a shared filesystem and offers a variety of batch schedulers such as AWS Batch and Slurm. 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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AWS ParallelCluster Cookbook
The Chef cookbook used to build and bootstrap AWS ParallelCluster
... 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, 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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TerraCognita
Reads from existing public and private cloud providers
Imports your current Cloud infrastructure to an Infrastructure As Code Terraform configuration (HCL) or/and to a Terraform State. At Cycloid, Infrastructure As Code is in the company's DNA since the beginning. To help our new customers adopt this best practice, we decided to build Terracognita to convert an existing infrastructure on Cloud Infrastructure into Terraform code in an automated way, relying on Terraform providers built by the community. We focused on AWS, GCP and Azure but Alibaba... -
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BBMap
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various 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... -
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Chimerax-UCSF
ChimeraX is an application for visualizing and analyzing molecule
ChimeraX is an application for visualizing and analyzing molecule structures such as proteins, RNA, DNA, lipids as well as gene sequences, electron microscopy maps, X-ray maps, 3D light microscopy and 3D medical imaging scans. It is the successor of the UCSF Chimera program. Example images and feature highlights show a few of its capabilities, and recipes show example command and Python API use. -
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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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CometAnalyser
CometAnalyser, for quantitative comet assay analysis.
Description: Comet assay provides an easy solution to estimate DNA damage in single cells through microscopy assessment. To obtain reproducible and reliable quantitative data, we developed an easy-to-use tool named CometAnalyser. CometAnalyser is an open-source deep-learning tool designed for the analysis of both fluorescent and silver-stained wide-field microscopy images. Once the comets are segmented and classified, several intensity/morphological features are automatically exported... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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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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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... -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering... -
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ExtAncSeqMEGA is a program to extract ancestral DNA sequences that have been calculated by MEGA. ExtAncSeqProt is a program to extract ancestral PROTEIN sequences that have been estimated by MEGA. See the ReadMe file for details and documentation
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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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Gemi
PCR primers / probes design from multiple & degenerate sequences
Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences... -
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aramultiomics
A toolkit for studying protein-protein/nucleic acid interaction
araMultiOmics consisted of seven modules where each module was created based on existing databases and software for studying protein binding sites/open chromatin regions, DNA-TF bonding profile, etc -
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popoolation
estimate natural variation and positive selection
PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D with a sliding window approach for chromosomes or for set of genes. One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https... -
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BioBytes PairSync
A Bioinformatics Tool for Basic Information Retrieval
This GUI app allows users to input biological sequences, either manually or by loading from a file. It supports DNA, RNA, and Protein sequences. Users can retrieve various information about the input sequence, such as nucleotide or amino acid frequency, GC content, reverse complement, transcription, translation, amino acid molecular weight, isoelectric point, and open reading frames. Users can save the output information to a text file and clear the output section for a clean slate... -
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janda
structural variant detector
Janda is a tool to detect structural variants in whole-genome DNA sequence data. It identifies structural variants (deletions, duplications, translocations, and inversions) using anomalously mapped pair reads and realigning potential junction reads. -
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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.