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https://bruskolab.diabetes.ufl.edu/research/handel-i/
HANDEL-1 program to better understand normal human immune development by acquiring stromal and mucosal tissues from infant and pediatric organ donors and to create novel and essential dataset informing immune system development in collaborative research project that leverages shared access to various tissues in conjunction with existing HANDEL-P program that seeks to understand development of pancreas and islet microenvironment in early life.
Proper citation: Human Atlas of Neonatal Development and Early Life Immunity (RRID:SCR_021947) Copy
https://edspace.american.edu/openbehavior/project/brainglobe/
Project is related to working with atlas data from multiple species on common platform.Provides collection of Python tools for working with atlas data from multiple species on common platform and for morphological analyses in systems neuroscience.
Proper citation: BrainGlobe project (RRID:SCR_021481) Copy
http://liorkirsch.github.io/brain-heatmap-web/
Custom Brain Heatmaps on top of the Allen Brain Atlas. Platform to generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing google spreadsheet template with specific brain region and gene information.
Proper citation: Brain heatmap (RRID:SCR_023815) Copy
https://research.nhgri.nih.gov/hydractinia/
Portal provides genomic and transcriptomic data for researchers interested in Hydractinia genomics and molecular biology. Includes browsers for the H. symbiolongicarpus and H. echinata genome assemblies and interactive interface for interrogating H. symbiolongicarpus single cell gene expression atlas. Provides gene pages with functional annotation data for every gene model for both species, including protein domain composition and orthology predictions.
Proper citation: Hydractinia Genome Project Portal (RRID:SCR_022602) Copy
https://scorch.igs.umaryland.edu/
Data coordination, analysis, and scientific outreach center to standardize and share single cell molecular HIV/SUD data by ensuring that data is FAIR. Program with mission of generating resources that would enable comprehensive tissue characterization at single cell level. This includes generating single nucleus transcriptomic data for identification of novel rare cell types, and enrichment of key cellular populations to inform pathophysiological understanding of CNS effects of SUD and HIV. Interdisciplinary effort, involving teams of investigators at ten institutions including Yale, Boston University, Mount Sinai, University of Nebraska Medical Center, Broad Institute, University of California San Diego, Weill Cornell Medicine, Allen Institute, Scripps Research as well as a Data Coordination Center hosted at Institute for Genome Sciences, University of Maryland Baltimore School of Medicine.
Proper citation: SCORCH (RRID:SCR_022600) Copy
https://edspace.american.edu/openbehavior/project/self-grooming-mice/
Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups.
Proper citation: Automated Classification of Self-grooming in Mice project (RRID:SCR_021597) Copy
https://edspace.american.edu/openbehavior/project/caiman/
Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis.
Proper citation: Calcium Imaging data Analysis project (RRID:SCR_021477) Copy
https://gitlab.orc.gmu.edu/kbijari/zebrafish-analysis-protocol
Project for quantitative neuronal morphometry by supervised and unsupervised learning. Includes protocol to quantify and interpret morphological properties of individual neurons reconstructed from microscopic imaging.Includes information about installation of analysis tools and downloading datasets and custom codes.
Proper citation: neuronal reconstruction analysis project (RRID:SCR_021638) Copy
https://www.fredhutch.org/en/research/shared-resources.html
Through Shared Resources, investigators in Fred Hutch/University of Washington Cancer Consortium and external academic and industry organizations can access services tailored to their specific research goals, including novel assay development or early access to new technologies.
Proper citation: Fred Hutchinson Cancer Center Shared Resources (RRID:SCR_022607) Copy
https://github.com/brentp/cyvcf2
Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.
Proper citation: cyvcf2 (RRID:SCR_024000) Copy
Interactive portal provides datasets, across variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. Provides comprehensive picture of genes and pathways affecting lipid droplet biology, including gene expression, proteomics, and LD morphology phenotypes, by integrating multiple relevant data types.
Proper citation: Lipid Droplet Knowledge Portal (RRID:SCR_021650) Copy
https://www.utsouthwestern.edu/labs/danuser/software/
Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences.
Proper citation: plusTipTracker (RRID:SCR_021890) Copy
Community led project to develop open, sustainable, usable, and unique identifier for every research organization in the world. Implementation of ROR IDs in scholarly infrastructure and metadata will enable more efficient discovery and tracking of research outputs across institutions and funding bodies.
Proper citation: Research Organization Registry (RRID:SCR_021891) Copy
Platform for data discovery to enhance the reuse of clinical neuroscience and neuroimaging data. Provides NeuroBridge ontology, and combines machine learning with ontology based search of both neuroimaging repositories like XNAT databases and open access full text journals such as PubMed Central. Connects researchers with potential neuroimaging data, by searching text of papers describing neuroimaging studies that contain information on neuroimaging data.
Proper citation: NeuroBridge (RRID:SCR_023703) Copy
http://fair.dei.unipd.it/software/
Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform.
Proper citation: Multimodal Environment for Neuroimaging and Genomic Analysis (RRID:SCR_023822) Copy
Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms.
Proper citation: SimpleITK (RRID:SCR_024693) Copy
https://github.com/khowe/quicktree/
Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.
Proper citation: quicktree (RRID:SCR_024205) Copy
http://colibread.inria.fr/software/mapsembler2/
Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.
Proper citation: Mapsembler2 (RRID:SCR_024102) Copy
https://github.com/gerddie/maxflow
Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.
Proper citation: MAXFLOW (RRID:SCR_024103) Copy
https://github.com/SciTools/cartopy
Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support.
Proper citation: Cartopy (RRID:SCR_024587) Copy
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