<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38304?offset=460 https://bioinformaticsonline.com/bookmarks/view/40721/efs-an-ensemble-feature-selection-tool-implemented-as-r-package-and-web-application Tue, 28 Jan 2020 05:12:23 -0600 https://bioinformaticsonline.com/bookmarks/view/40721/efs-an-ensemble-feature-selection-tool-implemented-as-r-package-and-web-application <![CDATA[EFS: an ensemble feature selection tool implemented as R-package and web-application]]> The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in EFS, which can be used separately or combined in an ensemble.

https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8

Address of the bookmark: http://efs.heiderlab.de/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs Tue, 30 Jun 2020 21:30:44 -0500 https://bioinformaticsonline.com/bookmarks/view/41916/truvari-structural-variant-comparison-tool-for-vcfs <![CDATA[truvari: Structural variant comparison tool for VCFs]]> Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42143/sibelia-a-comparative-genomics-tool Sat, 22 Aug 2020 02:49:00 -0500 https://bioinformaticsonline.com/bookmarks/view/42143/sibelia-a-comparative-genomics-tool <![CDATA[Sibelia: A comparative genomics tool]]> Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. 

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

More at http://bioinf.spbau.ru/sibelia

Sibelia docs http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md

Address of the bookmark: https://github.com/bioinf/Sibelia

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43120/ventoy-an-open-source-tool-to-create-bootable-usb-drive Tue, 29 Jun 2021 10:16:19 -0500 https://bioinformaticsonline.com/bookmarks/view/43120/ventoy-an-open-source-tool-to-create-bootable-usb-drive <![CDATA[Ventoy: an open source tool to create bootable USB drive]]> Ventoy is an open source tool to create bootable USB drive for ISO/WIM/IMG/VHD(x)/EFI files. With ventoy, you don't need to format the disk over and over, you just need to copy the image files to the USB drive and boot it. You can copy many image files at a time and ventoy will give you a boot menu to select them. x86 Legacy BIOS, IA32 UEFI, x86_64 UEFI, ARM64 UEFI and MIPS64EL UEFI are supported in the same way. Both MBR and GPT partition style are supported in the same way. Most type of OS supported(Windows/WinPE/Linux/Unix/Vmware/Xen...) 700+ ISO files are tested. 

Address of the bookmark: https://github.com/ventoy/Ventoy

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/43902/interactivenn-a-web-based-tool-for-the-analysis-of-sets-through-venn-diagrams Wed, 29 Jun 2022 03:22:26 -0500 https://bioinformaticsonline.com/bookmarks/view/43902/interactivenn-a-web-based-tool-for-the-analysis-of-sets-through-venn-diagrams <![CDATA[InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams]]> InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

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Address of the bookmark: http://www.interactivenn.net/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes Tue, 10 Sep 2024 04:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes <![CDATA[NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes]]> NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes 

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NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

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