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Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest.
Proper citation: Stan (RRID:SCR_018459) Copy
http://www.nitrc.org/projects/reprocontainers/
Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.
Proper citation: ReproNim/containers (RRID:SCR_018467) Copy
https://bioconductor.org/packages/ggtree/
Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.
Proper citation: ggtree (RRID:SCR_018560) Copy
http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx
Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.
Proper citation: DAMBE (RRID:SCR_018528) Copy
https://github.com/lmb-embrapa/machado
Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.
Proper citation: Machado (RRID:SCR_018428) Copy
https://github.com/OHDSI/CohortMethod
Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.
Proper citation: CohortMethod (RRID:SCR_018511) Copy
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
http://tools.dice-database.org/GOnet/)
Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.
Proper citation: GOnet (RRID:SCR_018977) Copy
http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/
Software Matlab toolbox to perform representational similarity analysis for neural data.
Proper citation: Toolbox for Representational Similarity Analysis (RRID:SCR_019029) Copy
https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation
Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer.
Proper citation: CLIP Tool Kit (RRID:SCR_019034) Copy
https://github.com/najasplus/hetindel_shinyapp
Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.
Proper citation: Hetindel (RRID:SCR_018922) Copy
Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.
Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
http://www.bioconductor.org/packages/release/bioc/html/affy.html
Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.
Proper citation: affy (RRID:SCR_012835) Copy
https://www.openicpsr.org/openicpsr/covid19
Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.
Proper citation: COVID-19 Data Repository (RRID:SCR_019105) Copy
https://trials.bgcarlisle.com/
Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set.
Proper citation: Clinical Trials Viewer (RRID:SCR_019230) Copy
Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.
Proper citation: PlasmoDB (RRID:SCR_013331) Copy
http://www.cytobank.org/index.html
A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.
Proper citation: Cytobank (RRID:SCR_014043) Copy
Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.
Proper citation: ChEMBL (RRID:SCR_014042) Copy
http://cerebrovascularportal.org
Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data.
Proper citation: Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
