The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Huiru Peng - One of the best experts on this subject based on the ideXlab platform.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    GigaScience, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    BACKGROUND The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new Genomic Variation data in diverse species. RESULTS Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale Genomic Variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence Variations. CONCLUSIONS SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    bioRxiv, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    Background: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers for exploring new Genomic Variation data in diverse species. Results: Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing and visualizing the large-scale Genomic Variation data that be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access SNPs/INDELs and annotation information by locus or gene and for user-defined sample sets through a webpage. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by SNPs/INDELs. Conclusions: SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in present studies. SnpHub and its tutorial are available as http://guoweilong.github.io/SnpHub/.

Wenxi Wang - One of the best experts on this subject based on the ideXlab platform.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    GigaScience, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    BACKGROUND The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new Genomic Variation data in diverse species. RESULTS Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale Genomic Variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence Variations. CONCLUSIONS SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    bioRxiv, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    Background: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers for exploring new Genomic Variation data in diverse species. Results: Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing and visualizing the large-scale Genomic Variation data that be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access SNPs/INDELs and annotation information by locus or gene and for user-defined sample sets through a webpage. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by SNPs/INDELs. Conclusions: SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in present studies. SnpHub and its tutorial are available as http://guoweilong.github.io/SnpHub/.

Zhaorong Hu - One of the best experts on this subject based on the ideXlab platform.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    GigaScience, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    BACKGROUND The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new Genomic Variation data in diverse species. RESULTS Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale Genomic Variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence Variations. CONCLUSIONS SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    bioRxiv, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    Background: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers for exploring new Genomic Variation data in diverse species. Results: Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing and visualizing the large-scale Genomic Variation data that be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access SNPs/INDELs and annotation information by locus or gene and for user-defined sample sets through a webpage. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by SNPs/INDELs. Conclusions: SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in present studies. SnpHub and its tutorial are available as http://guoweilong.github.io/SnpHub/.

Zihao Wang - One of the best experts on this subject based on the ideXlab platform.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    GigaScience, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    BACKGROUND The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new Genomic Variation data in diverse species. RESULTS Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale Genomic Variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence Variations. CONCLUSIONS SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    bioRxiv, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    Background: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers for exploring new Genomic Variation data in diverse species. Results: Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing and visualizing the large-scale Genomic Variation data that be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access SNPs/INDELs and annotation information by locus or gene and for user-defined sample sets through a webpage. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by SNPs/INDELs. Conclusions: SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in present studies. SnpHub and its tutorial are available as http://guoweilong.github.io/SnpHub/.

Xintong Li - One of the best experts on this subject based on the ideXlab platform.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    GigaScience, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    BACKGROUND The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new Genomic Variation data in diverse species. RESULTS Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale Genomic Variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence Variations. CONCLUSIONS SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/.

  • snphub an easy to set up web server framework for exploring large scale Genomic Variation data in the post Genomic era with applications in wheat
    bioRxiv, 2020
    Co-Authors: Wenxi Wang, Xintong Li, Zhongfu Ni, Zhaorong Hu, Zihao Wang, Huiru Peng
    Abstract:

    Background: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate Genomic Variations across hundreds or even thousands of samples in the post-Genomic era. The management and exploration of these large-scale Genomic Variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers for exploring new Genomic Variation data in diverse species. Results: Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing and visualizing the large-scale Genomic Variation data that be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access SNPs/INDELs and annotation information by locus or gene and for user-defined sample sets through a webpage. Users can freely analyse and visualize Genomic Variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by SNPs/INDELs. Conclusions: SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in present studies. SnpHub and its tutorial are available as http://guoweilong.github.io/SnpHub/.