Best Genomics Data Analysis Software in Japan

JADBio is an automated machine learning platform that uses JADBio's state-of-the art technology without any programming. It solves many open problems in machine-learning with its innovative algorithms. It is easy to use and can perform sophisticated and accurate machine learning analyses, even if you don't know any math, statistics or coding. It was specifically designed for life science data, particularly molecular data. It can handle the unique molecular data issues such as low sample sizes and high numbers of measured quantities, which could reach into the millions. It is essential for life scientists to identify the biomarkers and features that are predictive and important. They also need to know their roles and how they can help them understand the molecular mechanisms. Knowledge discovery is often more important that a predictive model. JADBio focuses on feature selection, and its interpretation.

OmicsBox, a leading bioinformatics tool, offers end-toend data analysis for genomes, transcriptomes and metagenomes. It also provides genetic variation studies. The application, which is used by leading private and public research institutes worldwide, allows researchers to process large and complicated data sets and streamline their analytical process. It is designed to be efficient, user-friendly and equipped with powerful tools to extract biological insight from omics data. The software is divided into modules, each of which has a set of tools and features designed to perform specific types of analyses, such as de novo genome assemblies, genetic variations analysis, differential expression analyses, taxonomic classifications, and taxonomic classes of microbiome, including the interpretation of results and rich visualizations. The functional analysis module uses the popular Blast2GO annotating methodology, making OmicsBox a great tool for non-model organisms research.

Interactive visualizations and analytics allow you to explore hundreds of single-cell transcriptome datasets as well as your own data. The software supports multimodal omics (e.g. CITE-seq and spatial transcriptomic. Explore the world's largest database of single-cell expression interactively. Access and query insights derived from a single cell database of millions of cells. The database is fully annotated, with cell type labels and experimental meta-data. BBrowser does not just create a portal to published works. It is an end-toend solution for YOUR single-cell data. Import your fastq, count matrices or Seurat objects and reveal the biological stories within. With a powerful package of visualizations, analyses and an intuitive interface you can easily mine insights from any single-cell dataset. Import data from single-cell CRISPR or Perturb-seq. Guide RNA sequences can be queried.

Geneious Prime makes bioinformatics more accessible by transforming raw information into visualizations which make sequence analysis intuitive. Simple assembly of sequences and easy editing contigs. Automatic annotation of gene prediction, motifs and translation. Genotype microsatellite trace with automated ladder fitting, peak calling, and generation of tables of alleles. A highly customizable sequence view displays beautiful visualizations of annotated assemblies and genomes. SNP variants analysis with powerful SNPs, RNA-Seq analysis and amplicon metagenomics. Create your own searchable database of primers for PCR and sequencing and design and test them. Geneious Biologics offers a flexible, scalable and secure way to streamline antibody analysis workflows. It allows you to create high-quality libraries, and select the best therapeutic candidates.

Design and simulate cloning processes accurately. Test complex projects, catch mistakes before they happen, get the right constructs on the first try. Cloning becomes easier when you see what you're doing. The intuitive interface simplifies complex tasks by providing you with a clear view of your work. SnapGene automates the documentation so you don't need to. Share and view every sequence edit or cloning process that led to the final plasmid. Improve your core molecular biological procedures and your results. SnapGene Academy, our new online learning centre, will help you master SnapGene as well as key concepts in cloning. SnapGene Academy contains over 50 video tutorials, taught by experts in the field. This helps you improve your skills in multiple molecular biological courses. SnapGene 7.2 offers a new visualization for primer homodimer structure and enhancements to the file management. Tabs can be organized using drag-and-drop in multiple windows.

The toolkit was developed in the Data Sciences Platform of the Broad Institute. It offers a variety of tools, with a focus on variant detection and genotyping. Its powerful processing engine, high-performance computing capabilities and flexibility make it a great tool for any project. The GATK is a standard in the industry for identifying SNPs in RNAseq and germline DNA data. Its scope has now expanded to include somatic short variation calling, copy number (CNV), and structural variation (SV). The GATK includes not only the variant callers, but also many utilities that perform related tasks like processing and quality-control of high-throughput sequence data. It also bundles the Picard toolkit. These tools were designed primarily to process whole genomes and exomes generated by Illumina sequencing technology. However, they can be adapted for a variety other technologies and experimental design.

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulatory in RNA-Seq sample. It accepts aligned RNA Sequence reads and assembles them into a minimal set of transcripts. Cufflinks estimates the relative abundances for these transcripts by calculating how many reads each one receives, while taking into account biases from library preparation protocols. Cufflinks is the result of a collaboration between the Laboratory for Mathematical and Computational Biology. We provide binary packages for Cufflinks to make the installation process easier. This saves users the sometimes frustrating task of building Cufflinks which requires you to install the libraries. Cufflinks comes with a number tools for analyzing RNASeq experiments. Some of these tools are standalone, while others form part of a larger workflow.

The Bioconductor Project aims to develop open source software that allows for repeatable and precise analysis of biological data. We encourage a collaborative and inclusive community of data scientists and developers. Resources to maximize Bioconductor's potential. Our tutorials, guides, documentation, and guides cover everything from basic functionality to advanced features. Bioconductor is an open-source and open-development software that uses the R statistical language. It has an active user base and two releases per year. Bioconductor offers Docker images with every release, and supports Bioconductor in AnVIL. Bioconductor, founded in 2001, is an open-source project widely used in bioinformatics. Over 1,000 developers have contributed over 2,000 R packages, which are downloaded over 40 million times per year. Bioconductor is cited in over 60,000 scientific publications.

Galaxy is a web-based, open-source platform for data-intensive biomedical studies. Start here if you are a new Galaxy user or consult our support resources. Install Galaxy yourself by following the tutorial. You can choose from thousands of tools in the tool shed. This instance of Galaxy uses infrastructure generously provided to it by the Texas Advanced Computing Center. Additional resources are available primarily via the Jetstream2 cloud, via ACCESS and with support from National Science Foundation. Quantify, visualize and summarize mismatches from deep sequencing data. Build maximum-likelihood trees. Phylogenomic/evolutionary tree construction from multiple sequences. Using TN-93, combine matching reads to form clusters. Remove sequences that are within a certain distance of a cluster from a reference. Estimate gene essentiality scores using maximum-likelihood.

Cellenics can help you turn your single-cell sequencing data into meaningful insights. Cellenics is an open-source analytics tool developed by Harvard Medical School for single cell RNA sequencing data. Biomage hosts the community instance. It allows biologists to explore datasets of single-cells without having to write code, and helps scientists and informaticians work together more effectively. It can take you from count matrixes to publication ready figures in a matter of hours. It can also be seamlessly integrated into your workflow. It is fast, interactive and user-friendly. It's cloud-based and scalable. Cellenics, hosted by Biomage as a community instance, is free for academics with small/medium datasets (upto 500,000 cells). Over 3000 academic researchers use it to study cancer, cardiovascular health and developmental biology.

Improve team productivity and generate greater returns on research. Interactive data visualization allows you to share private and public data with other teams. Rosalind is a multi-tenant SaaS designed for scientists. Analyze, share, interpret, plan, validate and generate new hypotheses. Code-free visualization, AI-powered interpretation, best-in-class collaboration. ROSALIND is suitable for scientists of all levels, since it does not require any programming or bioinformatics knowledge. ROSALIND's powerful downstream analysis and collaborative capabilities make it a platform for discovery and data hub that connects experiment design, quality assurance, and pathway exploration. ROSALIND manages tens or thousands of cores of computing and petabytes in storage to dynamically scale each experiment up and down to deliver results. Share results instantly with other scientists around the world with audit tracking, so everyone can concentrate on interpretation and not the processing.

This free tool provides stunning visualizations of genomic data, giving you the power to see exactly what is happening at each base pair within your samples. GenomeBrowse is a desktop application that runs natively on your computer. You no longer have to compromise on speed or interface quality in order to achieve a consistent experience across platforms. It was designed with performance in mind, to provide a faster browsing experience than any genome browser currently available. GenomeBrowse has also been integrated into the powerful Golden Helix VarSeq annotation and interpretation platform. VarSeq is a powerful tool for filtering, analyzing, and annotating your data. If you enjoy the visualization experience provided by GenomeBrowse then try it out. GB can show all your alignment data. You can find context-relevant findings by looking at all your samples together.

MEGA (Molecular Evolutionary Genetics Analysis), a powerful, user-friendly software package designed to analyze DNA and protein sequences from species and populations. It allows for both manual and automatic sequence alignment, phylogenetic trees inference, and evolutionary hypotheses testing. MEGA is a powerful tool for comparative analysis of sequences and understanding molecular evolutionary processes. It supports a wide range of statistical methods, including maximum likelihood, Bayesian Inference, and ordinary least-squares. MEGA has advanced features like real-time captions to explain the results of the analysis and the methods used. It also uses the maximum composite likelihood method to estimate evolutionary distances. The software comes with powerful visual tools such as the alignment/trace editors and tree explorers, and supports multi-threading to ensure efficient processing. MEGA is compatible with Windows, Linux and macOS.

Founded in order to improve lives through high-value care, the hc1 platform has become a leader in bioinformatics for precision prescribing and testing. The cloud-based hc1 high-value care platform® organizes large amounts of live data, including genomics and medications, to provide solutions that ensure the right patient receives the right test and prescription. The hc1 Platform is a platform that powers solutions that optimize diagnostic testing, prescribing, and patient care for millions of patients across the country. Visit www.hc1.com to learn more about the proven approach of hc1 to personalizing care and eliminating waste for thousands upon thousands of health systems, diagnostic labs, and health plans.

Universal Analysis Software (UAS), a platform that analyzes and manages forensic genomic data, simplifies complex bioinformatics. The UAS is an all-inclusive solution that includes analysis modules for all ForenSeq workflows, including ForenSeq MainstAY and ForenSeq Kintelligence. It also contains ForenSeq DNA Signature prep, ForenSeq DNA Whole Genome, ForenSeq Control Region, ForenSeq mtDNA Whole Genome and ForenSeq UAS Control Region. UAS quickly generates FASTQ files and performs alignment. It also calls forensically relevant variants using NGS data. The extensive testing behind UAS's variant calls ensures that they are reliable and deliver accurate results in a user-friendly package that does not require per-seat licenses. UAS is a tool for forensic analysts. It streamlines the handling of base-bybase sequence information. It also includes a variety of features that allow you to perform everything from a quick review of everyday STR profiles to detailed analysis on the most difficult samples.

PacBio (Pacific Biosciences) is a premier life science technology company that is designing, developing and manufacturing advanced sequencing solutions to help scientists and clinical researchers resolve genetically complex problems. Our products address solutions across a broad set of research applications including human germline sequencing, plant and animal sciences, infectious disease and microbiology, oncology, and other emerging applications. The Revio system adds affordability, high throughput, and ease of use to a foundation of long reads, exceptional accuracy, and direct methylation detection. The Onso system is an innovative benchtop short-read DNA sequencing platform with an extraordinary level of accuracy using PacBio sequencing by binding. Software tools for Sequel II/IIe and Revio systems designed to set up and monitor long-read HiFi sequencing runs, review performance metrics, analyze, visualize, and annotate sequencing data.

The QIAGEN CLC Geneomics Workbench is a powerful tool that works for all workflows. It is easy to overcome data analysis challenges with cutting-edge technology, unique features and algorithms that are widely used by scientists in industry and academia. Bioinformatics software solutions that are user-friendly allow for comprehensive analysis and interpretation of your NGS data. This includes de novo assembly and transcriptome assembly, resequencing analysis, WES and targeted panel support, variant calling, variant calling, RNA–seq, ChIP–seq and DNA methylation analysis (bisulfite sequence analysis). You can analyze your RNA-seq (miRNA, smallRNA) and smallRNA (lncRNA), data using easy-to-use transcriptomics workflows that allow for differential expression analysis at both gene and transcript levels. QIAGEN CLC Genomics Workbench was designed to support a wide variety of NGS bioinformatics programs.

Partek bioinformatics software provides powerful visualization and statistical tools in an intuitive interface. Researchers of all levels can explore genomic data faster and more efficiently than ever before. We turn data into discovery®. Our intuitive interface makes it easy for scientists to perform sophisticated array and NGS analysis using pre-installed workflows. Public and custom statistical algorithms can be used together to quickly and accurately distill NGS data into biological insights. Genome browser, Venn diagrams and heat maps, as well as other interactive visualizations, show the biology of your next generation sequencing and array data in vivid color. Our Ph.D. scientists can be reached at any time to assist with your NGS analysis. This product is specifically designed for next-generation sequencing applications that require high-level computing. It offers flexible installation and management options.

ESMFold demonstrates how AI can provide new tools for understanding the natural world. It is similar to the microscope which allowed us to see the world at a tiny scale and gave us a new understanding of the world. AI can help us see biology in a different way and understand the vastness of nature. AI research has largely focused on helping computers understand the world in a similar way to humans. The language of proteins is a language that is beyond human comprehension. Even the most powerful computational tools have failed to understand it. AI has the potential of opening up this language to our comprehension. AI can be studied in new domains like biology to gain a better understanding of artificial intelligence. Our research reveals connections across domains. Large language models that are behind machine translation, natural speech understanding, speech recognition, image generation, and machine translation are also able learn deep information about biology.

Vytelle is a precision livestock business that reshapes the way cattle producers around the world optimize their herds. Our solutions reduce uncertainty and help you make the most important decisions regarding reproduction and mating. Vytelle™, our proprietary individual animal data capture software, is VytelleSENSE™. It records feed intake and inpen weight gain to help you identify high-performing animals that exhibit important economic and environmental traits. Low-contact devices capture key performance data without stressing the animal and communicate it to other information for processing and integration. Our decision tools are powered by the only AI analytic engine in the industry, based on 30 years of continuous improvement in helping producers collect and use data about cattle. It quickly processes phenotypic and genomic data, as well as performance data, to create easy-to-read dashboards, reports, and reports that allow you to make better decisions for your cattle operation.

DNAnexus Titan™, a trusted data analysis solution, is the future of genomics and clinical pipelines. Legacy informatics tools are not designed to handle today's larger volumes of sequencing data. Research centers and clinical diagnostic test companies find it difficult to create, refine and validate pipelines using home-grown systems. DNAnexus Titan™ is a unified platform which removes bottlenecks from development and production. It brings all data and pipelines into one place, resulting in unparalleled efficiency. Let us handle the heavy lifting in managing industry- and region-specific compliance and security requirements, while meeting the global demand for sequencing information.

Persistence container technology allows for lightweight operation. Pay-per-use in just seconds, not hours or months. The next month, fees will be paid via credit card. Low price for high performance. Oak Ridge National Laboratory will install it in the fastest supercomputer in the world. Machine learning applications such as deep learning, computational fluid dynamic, video encoding and 3D graphics workstations, 3D renderings, VFXs, computational finance, seismic analyses, molecular modelling, genomics, and server-side GPU computing workloads.

Correlation Engine, an interactive omics database, places private omics data into a biological context by combining it with highly curated publicly available data. Correlation Engine, one of the largest databases in the world for life science research, provides researchers with unprecedented access and insight to a vast number of high-quality whole genome analyses. The knowledgebase allows for novel discoveries through the interrogation of billions of datapoints derived from standard analyses of whole genome studies. A suite of applications for determining biological context, a constantly growing library of curated datasets, and support of multiple species and multi-omic data sets. Use a simple graphical interface to leverage guided workflows and APIs. Accelerate the journey from omic to decision-making and gain access to more than 25,000 multi-omics studies that have been reanalyzed (from over 250.000 signatures).

Emedgene streamlines tertiary analyses for germline research and rare disease genomics. Emedgene was designed to speed up the time and certainty of user-defined variant interpretations, prioritizations, curations, and research reports. Automate your tertiary analyses with explainable AI and automation that supports genomes, exomes and virtual panels. Unify your NGS instruments and your IT systems in order to simplify and secure the entire workflow. With the latest knowledge graph options, curation abilities, and a team to support you, you can confidently keep up with evolving science, technologies, and demand. Automated workflows and explainable AI (XAI), which can be used to increase throughput without adding more staff, are a great way to do this. Implement a high-throughput WGS,WES, virtual panel or targeted panel workflow integrated into your lab's ecosystem.

Store, archive, and manage multi-omic data sets. Illumina Connected Analytics provides a secure platform for genomic data to operationalize informatics, and drive scientific insight. CWL and Nextflow allow you to easily import, build and edit workflows. Leverage DRAGEN bioinformatics pipelines. Organize your data in a safe workspace and share it with the world in a compliant way. Our platform allows you to keep your data in the cloud. Visualize and interpret data using a flexible analysis tool, such as JupyterLab Notebooks. Data warehouses allow you to aggregate, query and analyze sample data and population data. Scale analysis operations through the creation, validation, automation, and deployment of informatics pipelines. Reduce the time needed to analyze genomic data when quick results are a key factor. Enable comprehensive profiling for the identification of novel drug targets and biomarkers of drug response. Data can be transferred seamlessly from Illumina sequencing platforms.