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https://CRAN.R-project.org/package=tidyverse

Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.

Proper citation: tidyverse (RRID:SCR_019186) Copy   

•   Source: SciCrunch Registry

https://www.elektralabs.com/solutions/education

Free curriculum, resources, and research for those considering incorporation of remote health monitoring.

Proper citation: Elektra Academy (RRID:SCR_019234) Copy   

•   Source: SciCrunch Registry

https://github.com/sciensic/SCIGA

Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing.

Proper citation: SCIGA (RRID:SCR_021002) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=simr

Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.

Proper citation: SIMR (RRID:SCR_019287) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gbs2ploidy

Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework.

Proper citation: gbs2ploidy (RRID:SCR_019290) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=spdep

Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.

Proper citation: spdep (RRID:SCR_019294) Copy   

•   Source: SciCrunch Registry

https://github.com/Danis102/seqpac

Software R package for analysis of short sequenced reads. Framework for small RNA analysis in R using Sequence Based Counts.Can be applied on any type of data generated by large scale nucleotide sequencing, where user wish to maintain sequence integrity during whole analysis.

Proper citation: seqpac (RRID:SCR_021079) Copy   

•   Source: SciCrunch Registry

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https://biology-assets.anu.edu.au/GenAlEx/Welcome.html

Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level.

Proper citation: GenAlEx (RRID:SCR_021102) Copy   

•   Source: SciCrunch Registry

https://www.waters.com/waters/en_US/High-Definition-Imaging-(HDI)-Software/nav.htm?cid=134833914&locale=en_US

Software package contains data analysis and processing tools required for rapid and effective interrogation of imaging data. Allows for full integration of full spectrum molecular imaging experiments on SYNAPT family platforms, as well as DESI imaging on Xevo G2-XS QTof Mass Spectrometers, using single user interface.

Proper citation: Waters High Definition Imaging (RRID:SCR_021054) Copy   

•   Source: SciCrunch Registry

https://github.com/bahanonu/ciatah

Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.

Proper citation: calciumImagingAnalysis (RRID:SCR_021153) Copy   

•   Source: SciCrunch Registry

https://github.com/parkgilbong/Minhee_Analysis_Pack

Software package for detection and measurement of spontaneous synaptic events. Integrated software package for detection and management of spontaneous synaptic events. Used in neurophysiology to detect spontaneous postsynaptic currents, search and visualize them in custom way, and perform hypothesis testing of retrieved data.

Proper citation: Minhee Analysis Package (RRID:SCR_021250) Copy   

•   Source: SciCrunch Registry

http://www.nextprot.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2025. Human protein knowledge platform. Knowledge platform for human proteins selects and filters high throughput data pertinent to human proteins from UniProtKB. Extends UniProtKB/Swiss-Prot annotations for human proteins to include several new data types.

Proper citation: neXtProt (RRID:SCR_008911) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/sbo/

A set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web Services.

Proper citation: SBO (RRID:SCR_006753) Copy   

•   Source: SciCrunch Registry

http://www.radnet.ucla.edu/sections/DINR/index.htm

Annotated images of human brain derived from CT, MRI, angiography and post-mortem sections and drawings. Brain vasculature: arteries, arterioles, veins. Pathological specimens. Quizzes and general information on brain structures and clinical syndromes. Extensive collection of images, many from pathological conditions.

Proper citation: Salamons Neuroanatomy and Neurovasculature Web-Atlas Resource (RRID:SCR_007343) Copy   

•   Source: SciCrunch Registry

http://www.digitalfishlibrary.org/index.php

A database of 3D magnetic resonance (MRI) images of fish accessible to scientists, educators and the general public via the web. The Marine Vertebrate Collection at the Scripps Institution of Oceanography provides the majority of the DFL specimens.

Proper citation: Digital Fish Library (RRID:SCR_008338) Copy   

•   Source: SciCrunch Registry

http://www.mbl.org/videoscribbler/vscrib.html

VideoScribbler is a program that makes it possible to trace directly onto live video. It was developed to provide a way to outline and count cells in a video image. The program displays the live video image in a 640x480 window. Userrs can click and drag the mouse to outline cells, while releasing the mouse button will complete the outline and increment the "Object Count" display at the bottom of the window.

Proper citation: Videoscribbler (RRID:SCR_013607) Copy   

•   Source: SciCrunch Registry

https://www.idigbio.org

iDigBio is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public.

Proper citation: Integrated Digitized Biocollections (RRID:SCR_014336) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://omictools.com/dog-picker-tool

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software tool for general particle picking in the single-particle processing of unknown macromolecules. Reference free particle picker with ability to sort particles based on size or it can be used to bootstrap the creation of templates or training datasets for other particle pickers. Used to facilitate particle selection in single particle electron microscopy., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DoG picker (RRID:SCR_016655) Copy   

•   Source: SciCrunch Registry

http://www.cyflogic.com/

Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics.

Proper citation: Cyflogic (RRID:SCR_016635) Copy   

•   Source: SciCrunch Registry