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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.
Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data.
Proper citation: OpticalMapping.info (RRID:SCR_017146) Copy
https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#bewith
Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
Proper citation: BeWith (RRID:SCR_016573) Copy
https://glimmpse.samplesizeshop.org/#/
Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GLIMMPSE (RRID:SCR_016297) Copy
https://cran.r-project.org/web/packages/factoextra/index.html
R package from CRAN to extract and visualize the results of multivariate data analysis.
Proper citation: factoextra (RRID:SCR_016692) Copy
https://github.com/lufuhao/Gsnap2Augustus
Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap.
Proper citation: Gsnap2Augustus (RRID:SCR_017555) Copy
https://github.com/sreeramkannan/Shannon
Software tool for de novo transcriptome assembly from RNA-Seq data.
Proper citation: Shannon (RRID:SCR_017037) Copy
https://github.com/neurostuff/NiMARE
Software Python package for coordinate and image based meta analysis of neuroimaging data.
Proper citation: NiMARE (RRID:SCR_017398) Copy
https://www.iconplc.com/innovation/nonmem/
Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.
Proper citation: NONMEM (RRID:SCR_016986) Copy
https://github.com/ANGSD/ngsRelate
Software tool for estimating pairwise relatedness from next-generation sequencing data.
Proper citation: ngsRelate (RRID:SCR_016588) Copy
https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.
Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy
Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities.
Proper citation: Deltagraph (RRID:SCR_018084) Copy
https://github.com/csb-toolbox/CSB
Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.
Proper citation: Computational Structural Biology Toolbox (RRID:SCR_016065) Copy
https://github.com/satijalab/seurat
Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data.
Proper citation: Seurat (RRID:SCR_016341) Copy
https://swissmodel.expasy.org/
Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists.
Proper citation: SWISS-MODEL (RRID:SCR_018123) Copy
https://github.com/HajkD/LTRpred
Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format.
Proper citation: LTRpred (RRID:SCR_017031) Copy
https://www.niaid.nih.gov/diseases-conditions/coronaviruses
Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses.
Proper citation: NIAID Overview of Coronaviruses (RRID:SCR_018290) Copy
https://CRAN.R-project.org/package=emmeans
Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays.
Proper citation: emmeans (RRID:SCR_018734) Copy
https://github.com/slimsuite/diploidocus
Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly.
Proper citation: Diploidocus (RRID:SCR_021231) Copy
https://jump-cellpainting.broadinstitute.org
Consortium is creating new data driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics. Creates public data set to validate and scale up this image based drug discovery strategy. By coordinating assay procedures across partners, future created data will be well matched. Aims to make cell images as computable as genomes and transcriptomes.
Proper citation: JUMP Cell Painting Consortium (RRID:SCR_021868) Copy
https://gitlab.com/gernerlab/cytomap/-/wikis/home
Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.
Proper citation: CytoMAP (RRID:SCR_021227) Copy
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