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Software tool for macromolecular structure visualization. Molecular visualization framework to visualize crystallographic models of macromolecules. Used to visualize and create publication quality images of macromolecular structures with user friendly interfaces.
Proper citation: CueMol (RRID:SCR_019052) Copy
https://www.otago.ac.nz/chatterjee-lab/tools/index.html
Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity.
Proper citation: Differential Methylation Analysis Package (RRID:SCR_019148) Copy
https://github.com/Griffan/FASTQuick
Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation.
Proper citation: FASTQuick (RRID:SCR_019269) Copy
https://www.nurseshealthstudy.org/
Portal about prospective investigations into risk factors for major chronic diseases in women. Nurses were selected as study population because of their knowledge about health and their ability to provide complete and accurate information regarding various diseases, due to their nursing education.The largest longitudinal study of women. Started in 1976, involving 275000 participants.
Proper citation: Nurses Health Study (RRID:SCR_019144) Copy
https://github.com/mjin1812/SMART
Software tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets.
Proper citation: Semi-Manual Alignment to Reference Templates (RRID:SCR_019265) Copy
Research infrastructure for the EU Human Brain Project. Provides digital tools and services which can be used to address challenges in brain research and brain inspired technology development. Digital research infrastructure, created by EU-funded Human Brain Project, that gathers extensive range of data and tools for brain-related research. EBRAINS will capitalize on the work performed by the Human Brain Project teams in digital neuroscience, brain medicine, and brain-inspired technology.You can share your neuroscience data, models and software.
Proper citation: EBRAINS (RRID:SCR_019260) Copy
http://eidors3d.sourceforge.net
Free software algorithms for forward and inverse modelling for Electrical Impedance Tomography (EIT) and Diffusion based Optical Tomography, in medical and industrial settings, and to share data and promote collaboration between groups working these fields.
Proper citation: EIDORS:Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software (RRID:SCR_019262) Copy
Brings together Centers for Disease Control and Prevention, National Institutes of Health, Robert Wood Johnson Foundation, and U.S. Department of Agriculture to accelerate progress in reducing childhood obesity in America, to manage projects and reach common goals, to coordinate funding to make the most of available resources, to share insights and expertise to strengthen research. NCCOR focuses on efforts that have to benefit children, teens, and their families, and communities in which they live.
Proper citation: National Collaborative on Childhood Obesity Research (RRID:SCR_019150) Copy
Standalone application for 3D visualisation and manipulation of mathematical field models. Cmgui is part of Continuum Mechanics, Imaging, Signal processing, System identification mathematical modelling environment. Generic open source modelling and visualisation package used to enable researchers to visualise biomedical images alongside dynamic geometry fields from computer models of cells, tissues and organs.
Proper citation: CMGUI (RRID:SCR_019271) Copy
http://www.e-crisp.org/E-CRISP/
Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours.
Proper citation: E-CRISP (RRID:SCR_019088) Copy
DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.
Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy
http://cqb.pku.edu.cn/ZhuLab/DeePhage
Software tool to distinguish virulent and temperate phage derived sequences in metavirome data with deep learning approach. Used to identify virome sequences as temperate phage derived or virulent phage derived fragments.
Proper citation: DeePhage (RRID:SCR_019243) Copy
Open source software platform for studying fruit fly brain function, and for investigating fruit fly brain disease models that are highly relevant to mechanisms of human neurological and psychiatric disorders. Collaborative ecosystem for accelerating discovery of functional logic of fruit fly brain. Includes FlyBrainLab and BrainMapsViz. Stores and integrates fruit fly brain research data. Repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease. Open framework for fruit fly brain data processing and model execution.
Proper citation: Fruit Fly Brain Observatory (RRID:SCR_019244) Copy
https://alcazar.science.uu.nl/services/HADDOCK2.2/
Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2 offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface.
Proper citation: HADDOCK (RRID:SCR_019091) Copy
Silhouette images of animals, plants, and other life forms, available for reuse. Database stores reusable silhouette images and phylogenetic taxonomy of all organisms. Each image is associated with one or more taxonomic names and indicates roughly what ancestral member of each taxon looked like.
Proper citation: PhyloPic (RRID:SCR_019139) Copy
https://github.com/ylab-hi/ScanNeo
Open software pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large sized indels. Used for identifying indel derived neoantigens using RNA-Seq data.
Proper citation: ScanNeo (RRID:SCR_019253) Copy
https://www.mangold-international.com/en/products/software/behavior-research-with-mangold-interact
Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software.
Proper citation: Interact (RRID:SCR_019254) Copy
https://github.com/medema-group/bigslice
Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data.
Proper citation: BiG-SLiCE (RRID:SCR_019130) Copy
https://cran.r-project.org/package=cthist
Software tool for mass downloading of historical clinical trial data from ClinicalTrials.gov.
Proper citation: cthist (RRID:SCR_019229) Copy
https://cran.r-project.org/web/packages/igraph/
Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.
Proper citation: igraph (RRID:SCR_019225) Copy
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