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https://omabrowser.org/oma/

Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMA Orthology database (RRID:SCR_016425) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/HARP

Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.

Proper citation: HARP (RRID:SCR_016546) Copy   

•   Source: SciCrunch Registry

https://github.molgen.mpg.de/MPIBR-coattia/MatlabMain/tree/master/behaviorAnalysis/code/NSKtoolbox/externalToolboxes/kCSDv1

Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.

Proper citation: kCSD-Matlab (RRID:SCR_016424) Copy   

•   Source: SciCrunch Registry

https://lifescience.bioquant.com/

Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders.

Proper citation: BIOQUANT Life Science (RRID:SCR_016423) Copy   

•   Source: SciCrunch Registry

http://cajadb.neuro.ufrn.br

Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.

Proper citation: CajaDB (RRID:SCR_016506) Copy   

•   Source: SciCrunch Registry

https://www.genome.jp/tools/dinies/

Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.

Proper citation: DINIES (RRID:SCR_016505) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/vtraver/PNNsMiceMachineVision

Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective".

Proper citation: PNNsMiceMachineVision (RRID:SCR_016485) Copy   

•   Source: SciCrunch Registry

http://www.flywings.org.uk/morphoj_page.htm

Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data.

Proper citation: MorphoJ (RRID:SCR_016483) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000363.v16.p10

Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation.

Proper citation: SABRe CVD Initiative (RRID:SCR_016572) Copy   

•   Source: SciCrunch Registry

https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

Proper citation: 1000 Fungal Genome Project (RRID:SCR_016463) Copy   

•   Source: SciCrunch Registry

https://github.com/WGS-TB/MentaLiST

Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.

Proper citation: MentaLiST (RRID:SCR_016469) Copy   

•   Source: SciCrunch Registry

https://cistem.org/

Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

Proper citation: cisTEM (RRID:SCR_016502) Copy   

•   Source: SciCrunch Registry

http://gcm.wfcc.info/

Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.

Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy   

•   Source: SciCrunch Registry

https://imaps.genialis.com/iclip

Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions.

Proper citation: iMaps (RRID:SCR_016705) Copy   

•   Source: SciCrunch Registry

https://github.com/fbreitwieser/pavian

Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.

Proper citation: Pavian (RRID:SCR_016679) Copy   

•   Source: SciCrunch Registry

https://github.com/tomazc/iCount

Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.

Proper citation: iCount (RRID:SCR_016712) Copy   

•   Source: SciCrunch Registry

http://jefferis.github.io/nat/

Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.

Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy   

•   Source: SciCrunch Registry

http://www.bdbiosciences.com/us/instruments/research/cell-sorters/bd-influx/m/744777/features/software

Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems.

Proper citation: BD FACS Sortware sorter software (RRID:SCR_016722) Copy   

•   Source: SciCrunch Registry

http://vectormap.si.edu/

Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap.

Proper citation: VectorMap (RRID:SCR_016721) Copy   

•   Source: SciCrunch Registry

http://www.nbtltd.com/products/smi-begaze%E2%84%A2-analysis-software

Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results.

Proper citation: SMI BeGaze (RRID:SCR_016648) Copy   

•   Source: SciCrunch Registry