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https://dice-database.org

Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy   

•   Source: SciCrunch Registry

http://www.syglass.io

Software visualization tool for direct volume rendering with no segmentation required. Enables users to view, annotate and analyze 3D data in VR. Data visualization and annotation system that allows rendering of large, volumetric data in its true, three- or four-dimensional form.

Proper citation: syGlass (RRID:SCR_017961) Copy   

•   Source: SciCrunch Registry

https://github.com/uleroboticsgroup/SVCP4CDataset

Software tool to collect vulnerable source code from open-source repositories linked to SonarCloud. Dataset repository with tagged files with BufferOverflow features associated to source code repositories publicly available.

Proper citation: SonarCloud Vulnerable Code Prospector for C (RRID:SCR_018011) Copy   

•   Source: SciCrunch Registry

https://crispy.secondarymetabolites.org

Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction.

Proper citation: CRISPy-web (RRID:SCR_017970) Copy   

•   Source: SciCrunch Registry

https://github.com/AndreMacedo88/VEnCode

Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases.

Proper citation: VEnCode (RRID:SCR_018024) Copy   

•   Source: SciCrunch Registry

https://biit.cs.ut.ee/gprofiler/page/r

Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.

Proper citation: gProfiler2 (RRID:SCR_018190) Copy   

•   Source: SciCrunch Registry

https://view.qiime2.org/

Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided.

Proper citation: QIIME 2 View (RRID:SCR_018074) Copy   

•   Source: SciCrunch Registry

http://www.premierbiosoft.com/protein_quantification_software/index.html

Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS.

Proper citation: PremierBiosoft Proteo IQ Software (RRID:SCR_018072) Copy   

•   Source: SciCrunch Registry

http://circadb.hogeneschlab.org/

Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans.

Proper citation: CircaDB (RRID:SCR_018078) Copy   

•   Source: SciCrunch Registry

http://www.milesculabs.org/QuB.html

Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: QuB (RRID:SCR_018076) Copy   

•   Source: SciCrunch Registry

https://vivli.org/

Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials.

Proper citation: Vivli (RRID:SCR_018080) Copy   

•   Source: SciCrunch Registry

http://www.diploid.com/moon

Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.

Proper citation: MOON (RRID:SCR_018005) Copy   

•   Source: SciCrunch Registry

https://mc-stan.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bioinformatics.fh-hagenberg.at/site/index.php?id=17

Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria.

Proper citation: MS Amanda (RRID:SCR_018396) Copy   

•   Source: SciCrunch Registry

http://statistika.mfub.bg.ac.rs/interactive-dotplot/

Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets.

Proper citation: Interactive Dotplot (RRID:SCR_018329) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry

https://github.com/grecolab/TinderMIX

Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features.

Proper citation: TinderMIX (RRID:SCR_018364) Copy   

•   Source: SciCrunch Registry