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https://gillisweb.cshl.edu/Primate_MTG_coexp/

We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain.

Proper citation: Gene functional conservation across cell types and species (RRID:SCR_023292) Copy   

•   Source: SciCrunch Registry

https://yoda.yale.edu/

Project to promote and facilitate sharing of clinical trial data. Provides set of policies to set standards to enhance data availability and transparency in support of strong scientific research which aims to advance scientific and medical knowledge with goal of improving public health and healthcare delivery. Project has the final decision making rights regarding these policies and granting or denial of data requests, as per contractual agreements between the YODA Project and its partners.

Proper citation: Yoda Project (RRID:SCR_022761) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/toolboxes-ephys-analysis/

Portal includes compared several toolboxes for spike and LFP analysis, connectivity analysis, dimensionality reduction, and generalized linear modeling. Discussion about major features of software available for Python and MATLAB including Brainstorm, Chronux, Elephant, FieldTrip, gramm, Spike Viewer, and SPIKY. They include succinct tables for assessing system and program requirements, quality of documentation and support, and data types accepted by each toolbox.

Proper citation: Toolboxes for Spike and LFP Analysis project (RRID:SCR_021478) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/scintillate/

Project related to time series calcium imaging evaluation and pre-processing. Included open source graphical viewer for time series calcium imaging evaluation and pre-processing is provided by Swedish University scientists .

Proper citation: Scintillate project (RRID:SCR_021479) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/wave-surfer/

Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus.

Proper citation: Wave Surfer project (RRID:SCR_021476) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://lipiddroplet.org/

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   

•   Source: SciCrunch Registry

https://ror.org/

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   

•   Source: SciCrunch Registry

https://github.com/muriloHoracio/TERL

Software tool for classification of transposable elements by convolutional neural networks. Preprocesses and transforms one dimensional sequences into two dimensional space data, image like data of sequences, and apply it to deep convolutional neural networks.

Proper citation: TERL (RRID:SCR_022064) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/bonvision/

Project related to creating and controlling visual environments.Provided open source software package for creating and controlling visual environments was developed by University College London scientists.

Proper citation: BonVision project (RRID:SCR_021491) Copy   

•   Source: SciCrunch Registry

https://neurobridges.org/

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   

•   Source: SciCrunch Registry

https://www.cs.bham.ac.uk/~ibs/imzMLConverter/

Software tool for generating imzML. Allows conversion to imzML mass spectrometry imaging standard utilising mzML mass spectrometry standard as intermediary format.

Proper citation: imzMLConverter (RRID:SCR_021642) Copy   

•   Source: SciCrunch Registry

https://github.com/LaubachLab/MedParse

Software tool to read MedPC data into Python and Matlab. MedPC code for saving precise times of behavioral events and MatLab and Python functions to convert MedPC data into time event codes.

Proper citation: MedParse (RRID:SCR_021528) Copy   

•   Source: SciCrunch Registry

https://www.bioinformatics.org/~tryphon/populations/

Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.

Proper citation: Populations (RRID:SCR_024175) Copy   

•   Source: SciCrunch Registry