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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/clinwiki-org/clinwiki
Clinical trials database.
Proper citation: ClinWiki (RRID:SCR_021297) Copy
https://portal.brain-map.org/explore/seattle-alzheimers-disease
Open atlas based on single cell profiling technologies with quantitative neuropathology and deep clinical phenotyping from middle temporal gyrus from neurotypical reference brains and brains from SEA-AD aged cohort that span spectrum of Alzheimer’s disease. Produced via collaboration between Allen Institute for Brain Science, University of Washington Alzheimer Disease Research Center and Kaiser Permanente Washington Health Research Institute.
Proper citation: Seattle Alzheimer Disease Brain Cell Atlas (RRID:SCR_023110) Copy
https://gitlab.com/rosen-lab/white-adipose-atlas
Single cell atlas of human and mouse white adipose tissue.
Proper citation: White Adipose Atlas (RRID:SCR_023625) Copy
Open online platform for single cell RNA-seq. Provides data management and analytics. Used to analyze public and private datasets and you can choose between several best practices workflows and browse existing analyses.
Proper citation: FASTGenomics (RRID:SCR_022898) Copy
https://www.girinst.org/repbase/
Database of repetitive DNA elements.Database of prototypic sequences representing repetitive DNA from different eukaryotic species. Used in genome sequencing projects worldwide as reference collection for masking and annotation of repetitive DNA.
Proper citation: Repbase (RRID:SCR_021169) 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://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
Open database of polygenic scores and relevant metadata required for accurate application and evaluation. Used for reproducibility and systematic evaluation.
Proper citation: Polygenic Score Catalog (RRID:SCR_023558) 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
Component of Accelerating Medicines Partnership Common Metabolic Diseases being developed at University of California San Diego as part of larger consortium of academic, industry and non-profit institutions worldwide. Resource is based on software developed by ENCODE DCC at Stanford University. Atlas provides epigenomics and other functional genomics data to promote understanding of genetic basis of common metabolic diseases.
Proper citation: Common Metabolic Disease Genome Atlas (RRID:SCR_022983) 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
http://www.meduniwien.ac.at/allfam/
Database for classifying allergenic proteins into protein families.You can browse lists of allergen families restricted by allergen source (plants, animals, fungi, bacteria) and route of exposure (inhalation, ingestion etc.) or search for specific allergens, sources or protein families. Every allergen family entry is linked to description of biochemical properties and allergological significance of family members as well as list of key references related to this family.
Proper citation: AllFam (RRID:SCR_021276) Copy
Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted.
Proper citation: trinetx (RRID:SCR_022760) Copy
Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways.
Proper citation: OncoboxPD (RRID:SCR_023723) 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
Open source adaptive immune receptor genotype and haplotype database. Core collection is inferred from immune receptor repertoire sequences and genomically derived material. Provides customisable reports, which allow users to study gene and allele usage in various ways.
Proper citation: VDJbase (RRID:SCR_022599) Copy
https://github.com/CraigList056/iqas
Modeling document labels using Latent Dirichlet Allocation is component tool under Integrated Quality Assurance System of Camarines Sur Polytechnic Colleges which categorizes text of particular document and use it for auto-tagging.
Proper citation: IQAS (RRID:SCR_023146) Copy
http://yanglab.hzau.edu.cn/BnTIR
Searchable database of Brassiceae genomic data hosted on the website.
Proper citation: BnTIR (RRID:SCR_023021) Copy
Database system that provides phosphorylated sites and information about which substrates are phosphorylated by specific kinase and which extracellular stimuli activate or inhibit protein phosphorylation via intracellular signaling cascades.
Proper citation: Kinase Associated Neural Phospho Signaling (RRID:SCR_023659) Copy
Database includes newly released genome sequences of Brassiceae species and published genomic data of most other Brassicaceae species.Data can be browsed in JBrowse or searched in BLAST. Offers service of searching for syntenic genes, which are generated based on their syntenic relationships to genes in Arabidopsis thaliana. Regularly updated with newly released reference genomes.
Proper citation: Brassicaceae Database (RRID:SCR_023019) Copy
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