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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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
https://github.com/Mark-Kramer/Seizure-Waves
Analysis and modeling code for waves of seizure activity.
Proper citation: Seizure-Waves (RRID:SCR_017455) Copy
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
Software tool for experimental design, sample size determination and analysis by Tempest Technologies.
Proper citation: mysamplesize (RRID:SCR_017575) Copy
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
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
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
https://github.com/PriceLab/TReNA
Methods for reconstructing transcriptional regulatory networks.
Proper citation: TReNA (RRID:SCR_017458) Copy
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
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
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
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
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
https://github.com/padster/pyDynamo/
Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics.
Proper citation: Dynamo (RRID:SCR_017541) Copy
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
https://github.com/LaBiOS/Transcriptive
Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results.
Proper citation: Transcriptive (RRID:SCR_017545) Copy
Femto Pulse System separates large molecular weight DNA fragments and detects nucleic acids into femtogram range.Fragment analyzer that provides pulsed field power supply which allows large molecular weight DNA fragments to be separated and nucleic acids detected into femtogram range. Ability to separate high molecular weight DNA up to 165 kb and detect nucleic acids down to 50 fg per uL input concentration makes system ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low concentration samples.
Proper citation: Agilent: Femto Pulse System (RRID:SCR_018058) Copy
https://www.thermofisher.com/order/catalog/product/3730S#/3730S
Medium to high throughput genetic analyzer that performs DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Upgradeable to 96 capillaries.
Proper citation: Thermo Fisher: Applied Biosystems: 3730 Genetic Analyzer (RRID:SCR_018052) Copy
Refridgerated centrifuge with 18 place capacity rotor that accomdates low to medium capacity in 1.5 or 2.0 mL tubes and Microtainer. Speed allows for standard molecular biology applications. Compact size and quiet operation.
Proper citation: Eppendorf: 5418 R Centrifuge (RRID:SCR_018050) Copy
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
