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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CSpritz Resource Report Resource Website 1+ mentions |
CSpritz (RRID:SCR_021884) | data access protocol, software resource, web service | Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs. | Intrinsic protein disorder segments prediction, homology, secondary structure, linear motifs, annotation | Italian Ministry of Education ; University of Padova |
DOI:10.1093/nar/gkr411 | Free, Freely available | SCR_021884 | SciCrunch Registry | 2026-09-26 02:17:18 | 2 | |||||||||
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ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data analysis software, data processing software, data visualization software, software application, software resource | 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. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
BMBF ; German Cancer Research Center-Heidelberg Center for Personalized Oncology |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | SciCrunch Registry | 2026-09-26 02:17:15 | 3949 | ||||||
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Computational Structural Biology Toolbox Resource Report Resource Website |
Computational Structural Biology Toolbox (RRID:SCR_016065) | CSB | software library, software resource, software toolkit | 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. | software, library, Python, reading, storing, analysis, biomolecular, variety, statistical, analysis, bioinformatic |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft (DFG) grant HA 5918/1-1; Max Planck Society |
PMID:22942023 | Free, Available for download | OMICS_09827 | https://sources.debian.org/src/csb/ | SCR_016065 | SciCrunch Registry | Computational Structural Biology Toolbox (CSB), CSB Toolbox | 2026-09-26 02:17:13 | 0 | ||||
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SWISS-MODEL Resource Report Resource Website 1000+ mentions |
SWISS-MODEL (RRID:SCR_018123) | data access protocol, data or information resource, service resource, software resource, web service | 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. | 3D protein structure, homology modeling server, protein modeling, structural bioinformatics, automated comparative modeling, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: Swiss-PdbViewerDeepViewv4.0 has parent organization: University of Basel; Basel; Switzerland provides: SWISS-MODEL Repository |
PMID:12824332 | Free, Freely available | biotools:swiss-model_workspace, biotools:swiss_model | https://bio.tools/swiss_model, https://bio.tools/swiss-model_workspace | SCR_018123 | SciCrunch Registry | 2026-09-26 02:17:15 | 4218 | |||||||
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SIGNOR Resource Report Resource Website 50+ mentions |
SIGNOR (RRID:SCR_018485) | data or information resource, data repository, database, service resource, storage service resource | Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles. | Signal transduction data, signaling information, published data collection, activity flow, chemical inhibitor, human proteome, manually annotated data, protein, protein relationship, FAIR data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: REDIportal |
ELIXIR-IIB ; EMBL-EBI ; Italian Association for Cancer Research ; Italian Node of the European ELIXIR infrastructure |
PMID:31665520 | Free, Available for download, Freely available | biotools:signor | https://bio.tools/signor | SCR_018485 | SciCrunch Registry | SIGnaling Network Open Resource, SIGNOR 2.0 | 2026-09-26 02:17:16 | 61 | |||||
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LTRpred Resource Report Resource Website 1+ mentions |
LTRpred (RRID:SCR_017031) | data analysis software, data analytics software, data processing software, software application, software resource | 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. | LTR, retrotransposon, prediction, genome, assembly, functional, annotation | is related to: R Project for Statistical Computing | Free, Available to download, Freely available | https://hajkd.github.io/LTRpred/ | SCR_017031 | SciCrunch Registry | LTRpred(ict) | 2026-09-26 02:17:15 | 6 | ||||||||
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LabSolutions Resource Report Resource Website 50+ mentions |
LabSolutions (RRID:SCR_018241) | data analysis software, data processing software, software application, software resource | Software package for data analysis by Shimadzu Oceania. | Data analysis system, data analysis, Shimadzu Oceania | Restricted | SCR_018241 | SciCrunch Registry | LabSolutions Software | 2026-09-26 02:17:16 | 87 | ||||||||||
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RNAcompete Resource Report Resource Website 1+ mentions |
RNAcompete (RRID:SCR_015900) | data analysis software, data processing software, software application, software resource | Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rna, protein, interaction, binding, preference, rna-seq, recognition, rbp, k-mer, structured rna, unstructured rna, matlab |
uses: MATLAB has parent organization: University of Toronto; Ontario; Canada |
Canadian Foundation of Innovation ; CIHR MOP-14609; CIHR MOP-49451; CIHR MOP-93671; National Science and Engineering Research Council of Canada (NSERC) ; Natural Sciences and Engineering Research Council ; Ontario Genomics Institute ; Ontario Research Fund |
PMID:19561594 PMID:27956239 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_18668 | SCR_015900 | SciCrunch Registry | RNAcompete Tool | 2026-09-26 02:15:39 | 1 | ||||||
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Leica HCS A Resource Report Resource Website 1+ mentions |
Leica HCS A (RRID:SCR_015811) | data acquisition software, data processing software, image acquisition software, image processing software, software application, software resource | Software supporting Leica Microsystem microscopes by performing high content screening automation. The software combines the flexibility of a point-scanning confocal with the high speed of a camera-based widefield system to compensate for specimen drift, single object tracking and immersion fluid. | high content screening automation, automation, confocal, widefield, microscope, leica | Commercially available, Available for purchase, Demo available | SCR_015811 | SciCrunch Registry | Leica High Content Screening Automation, High Content Screening Automation Leica HCS A | 2026-09-26 02:15:38 | 1 | ||||||||||
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Cross-species scaffolding Resource Report Resource Website 1+ mentions |
Cross-species scaffolding (RRID:SCR_015932) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references. | mate, pair, end, reference, genome | Free, Available for download, Freely available | SCR_016125 | SCR_015932 | SciCrunch Registry | cross-species-scaffolding | 2026-09-26 02:15:39 | 1 | |||||||||
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End Sequence Analysis ToolKit (ESAT) Resource Report Resource Website 1+ mentions Rating or validation data |
End Sequence Analysis ToolKit (ESAT) (RRID:SCR_015812) | ESAT | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit, source code | Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends." | short read, rna-seq, expression analysis, dge, digital expression library, transcript end, sequence analysis, alignment, sam file, bam file | PMID:27470110 | Free, Available for download | SCR_015812 | SciCrunch Registry | End Sequence Analysis ToolKit | 2026-09-26 02:15:38 | 9 | ||||||||
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Neuroscan SynAmps RT 64-channel Amplifier Resource Report Resource Website 1+ mentions |
Neuroscan SynAmps RT 64-channel Amplifier (RRID:SCR_015818) | resource | Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300. | eeg, signal amplifier, signal amplification, 64 channel, neuroimaging, hardware, instrument, equipment | Commercially available, Available for purchase | SCR_015818 | SciCrunch Registry | 2026-09-26 02:15:38 | 7 | |||||||||||
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MicrobeTracker Resource Report Resource Website 100+ mentions |
MicrobeTracker (RRID:SCR_015939) | data processing software, image analysis software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them. | microbe, tracking, tracker, matlab, microscopy, microbiology, bacteria, cell, cell imaging, imaging, image, analysis |
uses: MATLAB requires: MATLAB |
SCR_015939 | SciCrunch Registry | 2026-09-26 02:15:39 | 119 | |||||||||||
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larvalign Resource Report Resource Website 1+ mentions |
larvalign (RRID:SCR_015815) | data analysis software, data or information resource, data processing software, data set, sequence analysis software, software application, software resource, software toolkit | Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping. | drosophila melanogaster, computational method, gene expression, alignment, larval brain, larvae, template generation, mapping, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download | biotools:larvalign | https://bio.tools/larvalign | SCR_015815 | SciCrunch Registry | 2026-09-26 02:15:38 | 1 | ||||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | consortium, data or information resource, organization portal, portal | Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains. | cell census, neuroscience, brain, brain initiative cell census network, whole mouse brain, |
uses: QuickNII uses: HistoloZee uses: CellLocator uses: Semi-Manual Alignment to Reference Templates uses: LoomPy uses: Cytosplore Viewer uses: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) uses: Blue Brain Cell Atlas uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Hippocampome.org uses: Neuron Phenotype Ontology uses: Brain Image Library uses: Distributed Archives for Neurophysiology Data Integration uses: NeuroMorpho.Org uses: Azimuth uses: Brain Observatory Storage Service and Database (BossDB) uses: Optimus Pipeline uses: scATAC Pipeline uses: Smart-seq2 Single Nucleus Multi Sample Pipeline uses: CEMBA MethylC Seq Pipeline uses: Brain Architecture Project uses: Single Cell Portal uses: MorphoHub uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Mouse Connectome Project uses: Allen Mouse Brain Reference Atlas uses: Allen Mouse Brain Common Coordinate Framework uses: Allen Human Reference Atlas, 3D, 2020 uses: NeMO Analytics uses: ANTS - Advanced Normalization ToolS uses: CloudReg uses: Brainome portal uses: CATlas uses: MetaNeighbor uses: Cell Annotation Platform uses: cellxgene uses: Neuroglancer uses: Vaa3D uses: QuickNII and VisuAlign uses: Hi5App uses: CloudVolume uses: neuroXiv uses: Brain Data Standards Ontology uses: Pittsburgh Supercomputing Center uses: Molecular Biosensor and Imaging Center uses: Generative Diffeomorphic Mapping uses: NIH NeuroBioBank uses: NeMOarchive lists: ccf_streamlines is related to: Mouse Connectome Project is related to: BarensLab Mini-Atlas is related to: Cumulus is related to: Pegasus is related to: Cirrocumulus is related to: Gene functional conservation across cell types and species is related to: BRAIN Initiative Cell Atlas Network is related to: ATAC Pipeline is related to: Slide-seq Pipeline is related to: Brain Knowledge Platform has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science provides: mBrainAligner provides: BICCN Cell Registry provides: Cell Type Knowledge Explorer provides: Epiviz has organization facet: BICCN Anatomy and Morphology Project has organization facet: Cell Type Knowledge Explorer has organization facet: mBrainAligner has organization facet: Terra has organization facet: Allen Brain Cell Atlas has organization facet: Multiome Pipeline has organization facet: Allen Software Development Kit has organization facet: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: BuildIndices has organization facet: MapMyCells |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | SciCrunch Registry | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-09-26 02:15:38 | 234 | |||||
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Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | data analysis software, data processing software, software application, software resource | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | SciCrunch Registry | 2026-09-26 02:15:39 | 32 | ||||||||||
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Feeding Experimentation Device project Resource Report Resource Website 1+ mentions |
Feeding Experimentation Device project (RRID:SCR_015942) | FED | data or information resource, portal, topical portal | Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging. | Feeding, food intake, optogenetic, behavioral data analysis, data analysis software, behavior apparatus, behavior rig, reward delivery, behavior measurement, homecage, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: Washington University in St. Louis; Missouri; USA |
NIH | PMID:27060385 | Commercially available | https://github.com/KravitzLab/FED1, https://edspace.american.edu/openbehavior/project/feeding-experimentation-device/, https://hackaday.io/project/72964-feeding-experimentation-device-fed-20 | SCR_015942 | SciCrunch Registry | , FED1, FED2, Feeding Experimentation Device system, Feeding Experimentation Device | 2026-09-26 02:15:39 | 1 | |||||
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Gblocks Resource Report Resource Website 1000+ mentions |
Gblocks (RRID:SCR_015945) | software application, software resource, standalone software, web application | Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | position, dna, protein, align, alignment, phylogenetic, analysis, block, ansi c, deletion, removal | is listed by: SoftCite | Desarrollo e Innovación Tecnológica ; Fundación BBVA ; Plan Nacional de Investigación Científica BIO2002-04426-C02-02 |
PMID:10742046 PMID:17654362 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015945 | SciCrunch Registry | 2026-09-26 02:15:39 | 2043 | ||||||||
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BioVoxxel Toolbox Resource Report Resource Website 10+ mentions |
BioVoxxel Toolbox (RRID:SCR_015825) | data processing software, image analysis software, software application, software resource, software toolkit | Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis. | microscopic image analysis, image filtering, image segmentation, binary processing, binary analysis, particle analysis |
is related to: ImageJ is a plug in for: ImageJ is a plug in for: Fiji/ImageJ is a plug in for: Fiji |
Free, Available for download | https://imagej.net/BioVoxxel_Toolbox, https://github.com/biovoxxel/BioVoxxel_Toolbox | SCR_015825 | SciCrunch Registry | BioVoxxel, BioVoxxel Toolbox (ImageJ/Fiji) | 2026-09-26 02:15:38 | 33 | ||||||||
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TreeDyn Resource Report Resource Website 100+ mentions |
TreeDyn (RRID:SCR_015946) | data processing software, data visualization software, software application, software resource | Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tree, variable, annotation, metainfo, newick, topology, graphic, operator, projection, localization, reflection, leaf, label, bio.tools |
is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:treedyn | https://bio.tools/treedyn | SCR_015946 | SciCrunch Registry | 2026-09-26 02:15:39 | 357 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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