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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://web.stanford.edu/group/dlab/optogenetics/
Database of different optogenetics resources like hardware, protocols, sequence information.
Proper citation: Optogenetics Resource Center (RRID:SCR_017513) Copy
https://www.estimationstats.com/#/
Web application for data analysis and visualizing effect sizes. Data analysis with estimation graphics.
Proper citation: Estimation Stats (RRID:SCR_018321) Copy
http://www.diabetesbiobank.org
Non-profit initiative of the Belgian Diabetes Registry (BDR), the Beta Cell Therapy consortium (BCT), the Flemish Center for Medical Innovation (CMI) and the Brussels Institute for Research and Innovation (Innoviris). It aims to support medical research into the epidemiology, prevention, diagnosis and treatment of diabetes.
Proper citation: Diabetes Biobank Brussels (RRID:SCR_015571) Copy
https://github.com/hash-bang/Reflib-Node
Reference library processing for JavaScript. Reference library processing for NodeJS.
Proper citation: RefLib (RRID:SCR_018320) Copy
https://hcup-us.ahrq.gov/nisoverview.jsp
Family of healthcare databases and related software tools and products developed through Federal-State-Industry partnership. Databases bring together data collection of State data organizations, hospital associations, private data organizations, and Federal government to create national information resource of encounter-level healthcare data. HCUP includes largest collection of longitudinal hospital care data in the United States, with all-payer, encounter-level information beginning in 1988. These databases enable research on broad range of health policy issues, including cost and quality of health services, medical practice patterns, access to healthcare programs, and outcomes of treatments at the national, State, and local market levels.
Proper citation: Healthcare Cost and Utilization Project (RRID:SCR_024410) Copy
http://www.technicalreports.org/trail/search/
Repository of technical reports from US government. Identifies, acquires, catalogs, digitizes and provides unrestricted access to U.S. government agency technical reports. Ensures preservation, discoverability, and persistent open access to government technical publications regardless of form or format. Search interface is hosted by University of Washington and searches all TRAIL content found at HathiTrust and UNT.
Proper citation: Trail Technical Report Archive (RRID:SCR_017324) Copy
https://rdrr.io/cran/WGCNA/man/BrainRegionMarkers.html
Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas.
Proper citation: BrainRegionMarkers (RRID:SCR_023836) Copy
https://ualr.edu/bioinformatics/midsouth-bioinformatics-center/
Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice.
Proper citation: University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) Copy
https://github.com/benfulcher/GCEA_FalsePositives
Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data.
Proper citation: GCEA_FalsePositives (RRID:SCR_023835) Copy
Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information.
Proper citation: HmtVar (RRID:SCR_017288) Copy
https://github.com/LeonDLotter/ABAnnotate/tree/v0.1.0
Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles.
Proper citation: ABAnnotate (RRID:SCR_023833) Copy
http://s-quest.bihealth.org/fiddle/
Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community.
Proper citation: fiddle (RRID:SCR_017327) Copy
It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.
Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy
https://github.com/BlueBrain/atlas-densities
Software tools to compute densities in context of brain atlases. Used to create BBP Cell Atlas, using Allen Mouse Brain Atlas and collected literature density values.Provides list of volumetric files that provides cell type density estimates for each voxel of mouse brain volume.
Proper citation: Atlas Densities (RRID:SCR_023839) Copy
https://figshare.com/articles/phi_toolbox_zip/3203326
Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation.
Proper citation: Phi Toolbox (RRID:SCR_015549) Copy
http://www.humphreyslab.com/SingleCell/
Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website.
Proper citation: Kidney Interactive Transcriptomics (RRID:SCR_017209) Copy
http://bioconductor.org/packages/EGSEA/
Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.
Proper citation: EGSEA (RRID:SCR_015036) Copy
https://github.com/BlueBrain/atlas-alignment-meter
Software Python CLI and library to measure jaggyness of brain parcellation volume. Used to measure slice-to-slice jaggedness of volumetric dataset, only in form of NRRD file.
Proper citation: Atlas Alignment Meter (RRID:SCR_023843) Copy
https://www.genome.jp/kegg/pathway.html
Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development.
Proper citation: KEGG PATHWAY Database (RRID:SCR_018145) Copy
http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH
Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt.
Proper citation: Embassy-domsearch (RRID:SCR_016086) Copy
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