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https://www.fastgenomics.org/

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   

•   Source: SciCrunch Registry

https://vertebrate.genenames.org/

Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.

Proper citation: VGNC (RRID:SCR_017514) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/

Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments.

Proper citation: Robot Reviewer (RRID:SCR_018961) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://csdb.glycoscience.ru/database/

Database contains manually curated natural carbohydrate structures, taxonomy, bibliography, NMR data. Bacterial and Plant and Fungal databases were merged to improve quality of content-dependent services, such as taxon clustering or NMR simulation. These separate databases will be supported in parallel until 2020.

Proper citation: Carbohydrate Structure Database (RRID:SCR_018684) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://trinetx.com/

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   

•   Source: SciCrunch Registry

http://bloodexposome.org

Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.

Proper citation: Blood Exposome Database (RRID:SCR_017610) Copy   

•   Source: SciCrunch Registry

https://vdjbase.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://yanglab.hzau.edu.cn/BnTIR

Searchable database of Brassiceae genomic data hosted on the website.

Proper citation: BnTIR (RRID:SCR_023021) Copy   

•   Source: SciCrunch Registry

https://www.alzforum.org/alzpedia

Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge.

Proper citation: ALZPEDIA (RRID:SCR_017548) Copy   

•   Source: SciCrunch Registry

http://brassicadb.cn

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   

•   Source: SciCrunch Registry

http://www.atcc.org/STR_Database.aspx

Comprehensive database of Short Tandem Repeat DNA profiles for all of ATCC human cell lines. ATCC data collection as part of continuing efforts to characterize and authenticate cell lines in Cell Biology collection.

Proper citation: ATCC STR database (RRID:SCR_019203) Copy   

•   Source: SciCrunch Registry

https://panglaodb.se/

Database for exploration of single cell RNA sequencing experiments from mouse and human. Collects and integrate data from multiple studies and present them through unified framework.

Proper citation: PanglaoDB (RRID:SCR_022580) Copy   

•   Source: SciCrunch Registry

http://omicslab.genetics.ac.cn/dred/index.php

Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest.

Proper citation: Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) Copy   

•   Source: SciCrunch Registry

http://www.mqtldb.org/

Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).

Proper citation: mqtldb (RRID:SCR_018002) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.biol.rug.nl/standalone/fiva/

Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) Copy   

•   Source: SciCrunch Registry