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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://kidsfirstdrc.org/portal/portal-features/
Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.
Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy
https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#bewith
Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
Proper citation: BeWith (RRID:SCR_016573) Copy
http://www.genetherapyreview.com/gene-therapy-research
The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.
Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://www.mousephenotype.org/imits/
This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products.
Proper citation: iMITS (RRID:SCR_016552) Copy
https://emcore.ucsf.edu/cryoem-software
Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux.
Proper citation: MotionCor2 (RRID:SCR_016499) 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
https://www.ncbi.nlm.nih.gov/projects/mutagene/
Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.
Proper citation: MutaGene (RRID:SCR_016574) 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
https://commonfund.nih.gov/hubmap
Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.
Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy
https://blake.bcm.edu/emanwiki/EMAN2
Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.
Proper citation: EMAN (RRID:SCR_016867) Copy
https://github.com/dpeerlab/phenograph
Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.
Proper citation: Phenograph (RRID:SCR_016919) Copy
Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols.
Proper citation: BICCN Cell Registry (RRID:SCR_017267) Copy
A database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials.
Proper citation: National Database for Clinical Trials related to Mental Illness (RRID:SCR_013795) Copy
http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/
A web application which serves as an alternate way to read scientific literature in PubMed Central and Bookshelf. PubReader features an easy-to-read multi-column display, a figure strip for access to figures, and a search function. It is designed especially to support reading on tablets and other smaller devices but is available for reading on laptops and desktops.
Proper citation: PubReader (RRID:SCR_013814) Copy
A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems.
Proper citation: BioPSE (RRID:SCR_014044) Copy
Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data.
Proper citation: Musculoskeletal Knowledge Portal (RRID:SCR_023171) Copy
http://www.nitrc.org/projects/gscca_2013/
Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.
Proper citation: Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) Copy
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