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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.
Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph.
Proper citation: VPV (RRID:SCR_016545) Copy
https://cm.jefferson.edu/rna22/
Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.
Proper citation: RNA22 (RRID:SCR_016507) Copy
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Proper citation: PaVE (RRID:SCR_016599) Copy
https://tbportals.niaid.nih.gov
Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.
Proper citation: TB PORTALS (RRID:SCR_016594) Copy
Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies.
Proper citation: TRIAGE (RRID:SCR_016609) Copy
Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi.
Proper citation: UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) Copy
http://www.indecbiosystems.com/imagingworkbench/default.asp
Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems.
Proper citation: Imaging WorkBench (RRID:SCR_016589) Copy
https://sleepdata.org/datasets/bestair/
Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.
Proper citation: Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) Copy
Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.
Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy
http://carolina.imis.athena-innovation.gr/mirextra/
Software tool for analysis of expression data for microRNA function.
Proper citation: DIANA-mirExTra (RRID:SCR_017498) Copy
http://neurocics.udd.cl/LANtoolbox.html
Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB.
Proper citation: LAN toolbox (RRID:SCR_017629) Copy
https://bioconductor.org/packages/TCGAbiolinks/
Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.
Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy
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
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://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
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://www.mbfbioscience.com/wormlab
Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays.
Proper citation: Worm Lab (RRID:SCR_017669) Copy
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