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https://neuron.yale.edu/neuron/

Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software.

Proper citation: NEURON (RRID:SCR_017449) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/atlases-and-data/rnaseq

Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus.

Proper citation: Transcriptomics Explorer (RRID:SCR_017567) Copy   

•   Source: SciCrunch Registry

Issue

https://www.nature.com/articles/nprot.2014.042

Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889.

Proper citation: Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) Copy   

•   Source: SciCrunch Registry

https://swmath.org/

Repository of math software. Information service for mathematical software. Provides access to database of information on mathematical software and includes systematic linking of software packages with relevant mathematical publications. Database for references on mathematical software.

Proper citation: swMath (RRID:SCR_017607) Copy   

•   Source: SciCrunch Registry

https://github.com/gdancik/shinyGEO

Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets.

Proper citation: shinyGEO (RRID:SCR_017605) Copy   

•   Source: SciCrunch Registry

http://geneatlas.roslin.ed.ac.uk

Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits.

Proper citation: GeneATLAS (RRID:SCR_017577) Copy   

•   Source: SciCrunch Registry

https://github.com/Mark-Kramer/Seizure-Waves

Analysis and modeling code for waves of seizure activity.

Proper citation: Seizure-Waves (RRID:SCR_017455) Copy   

•   Source: SciCrunch Registry

https://github.com/SciCrunch/SciGraph

Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal.

Proper citation: SciGraph (RRID:SCR_017576) Copy   

•   Source: SciCrunch Registry

http://www.mysamplesize.com

Software tool for experimental design, sample size determination and analysis by Tempest Technologies.

Proper citation: mysamplesize (RRID:SCR_017575) Copy   

•   Source: SciCrunch Registry

http://refgenie.databio.org

Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis.

Proper citation: refgenie (RRID:SCR_017574) Copy   

•   Source: SciCrunch Registry

https://leora-software.com/products/poloplusonline

Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB.

Proper citation: PoloPlus USB Drive software (RRID:SCR_017614) Copy   

•   Source: SciCrunch Registry

http://statpackets.org/

Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together.

Proper citation: StatPackets (RRID:SCR_017613) Copy   

•   Source: SciCrunch Registry

https://github.com/PriceLab/TReNA

Methods for reconstructing transcriptional regulatory networks.

Proper citation: TReNA (RRID:SCR_017458) Copy   

•   Source: SciCrunch Registry

https://kg.ebrains.eu/

Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.

Proper citation: EBRAINS Knowledge Graph (RRID:SCR_017612) Copy   

•   Source: SciCrunch Registry

http://www.immunexpresso.org

Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions.

Proper citation: immuneXpresso (RRID:SCR_017578) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rjags/index.html

Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

Proper citation: rjags (RRID:SCR_017573) Copy   

•   Source: SciCrunch Registry

http://project-dare.eu/

EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously.

Proper citation: Project DARE (RRID:SCR_017538) Copy   

•   Source: SciCrunch Registry

https://www.leicabiosystems.com/histology-equipment/cryostats/leica-cm1520/

Cryostat for routine histology and cryosectioning including critical applications such as Mohs surgery. Brain sectioning. Actively cooled quick freezing shelf with defrost function and refrigeration system are provided.

Proper citation: Leica: CM1520 Cryostat (RRID:SCR_017543) Copy   

•   Source: SciCrunch Registry

https://github.com/padster/pyDynamo/

Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics.

Proper citation: Dynamo (RRID:SCR_017541) Copy   

•   Source: SciCrunch Registry

https://scdevdb.deepomics.org/

Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes.

Proper citation: Single Cell Developmental Database (RRID:SCR_017546) Copy   

•   Source: SciCrunch Registry