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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://imputationserver.sph.umich.edu/index.html#!pages/home
Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.
Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy
Web tool to classify citation statements from scientific articles using deep learning. Used for discovering and evaluating scientific articles via Smart Citations.
Proper citation: scite (RRID:SCR_018568) Copy
https://github.com/denisecailab/minian
Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.
Proper citation: Minian (RRID:SCR_022601) Copy
https://github.com/ABCD-STUDY/simple-t1-motion-detection
Software to measure the amount of ghosting artifacts in T1-weighted DICOM images. This program reads DICOM images and calculates a measure of the noise structure in one part of the image.
Proper citation: simple-t1-motion-detection (RRID:SCR_016022) Copy
A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality.
Proper citation: Spark (RRID:SCR_006207) Copy
Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload.
Proper citation: Antibody Registry (RRID:SCR_006397) Copy
Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.
Proper citation: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) Copy
Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols.
Proper citation: Phenotypes and eXposures Toolkit (RRID:SCR_006532) Copy
http://cancercontrol.cancer.gov/tcrb/tturc/
A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment.
Proper citation: Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST
Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.
Proper citation: FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) Copy
https://github.com/ABCD-STUDY/delay-discounting
Software that performs a delay-discounting task measuring impulsivity. Used in ABCD study.
Proper citation: delay-discounting (RRID:SCR_016031) Copy
Software that generates container-based behavioral experiments for reproducible science. It offers a library of experiments, games, and surveys, support for multiple kinds of databases, and robust documentation for the provided tools.
Proper citation: The Experiment Factory (RRID:SCR_016107) Copy
https://reprint-apms.org/?q=chooseworkflow
Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.
Proper citation: CRAPome (RRID:SCR_025008) Copy
https://github.com/calico/borzoi
Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.
Proper citation: Borzoi (RRID:SCR_026619) Copy
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