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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | software application, image analysis software, software resource, data processing software | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-07-27 09:35:15 | 13 | ||||||
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SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | software application, image analysis software, software resource, data processing software | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | NIH ; NLM ; LHNCBC HHSN276201500692P |
Free, Available for download | SCR_016215 | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-07-27 09:35:15 | 4 | |||||||||
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cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | software application, image analysis software, software resource, data processing software | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-07-27 09:35:18 | 2480 | |||||||||
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BZ-H3A analyzer software Resource Report Resource Website 10+ mentions |
BZ-H3A analyzer software (RRID:SCR_017375) | software application, image analysis software, software resource, data processing software | Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series. | Analysis, Keyence, Japan, fluorescence, microscope, BZ-X | SCR_017375 | 2026-07-27 09:35:29 | 10 | ||||||||||||
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Image Quant TL Resource Report Resource Website 100+ mentions |
Image Quant TL (RRID:SCR_018374) | software application, image analysis software, software resource, data processing software | Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting. | Image analysis, Cytiva, image, electrophoresis gel image, blot image, array, colony count image, analysis | SCR_018374 | , Image Quant TL array analysis, ImageQuant TL 8.2 | 2026-07-27 09:35:44 | 381 | |||||||||||
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UN-SCAN-IT Gel Analysis Software Resource Report Resource Website 1+ mentions |
UN-SCAN-IT Gel Analysis Software (RRID:SCR_017291) | software application, image analysis software, software resource, data processing software | Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC. | electrophoresis, gel, image, analysis, density, quantification, Silk Scientific Inc | Restricted | SCR_017291 | 2026-07-27 09:35:28 | 9 | |||||||||||
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Stereo Investigator - Whole Slide Edition Resource Report Resource Website 1+ mentions |
Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) | software application, image analysis software, software resource, data processing software | Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses. | Quantitative, analysis, stereology, whole, slide, image, MBF Bioscience | Restricted | SCR_017667 | 2026-07-27 09:35:32 | 3 | |||||||||||
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HALO Resource Report Resource Website 50+ mentions |
HALO (RRID:SCR_018350) | HALO | software application, image analysis software, software resource, data processing software | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-07-27 09:35:43 | 77 | ||||||||
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IncuCyte® Chemotaxis Software Resource Report Resource Website 10+ mentions |
IncuCyte® Chemotaxis Software (RRID:SCR_017316) | software application, image analysis software, software resource, data processing software | IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate. | Add-on, module, IncuCyte ZOOM, live-cell, analysis, system, ClearView, Chemotaxis, Plate, Essen Bioscience, Sartorius | is provided by: Sartorius | Restricted | SCR_017316 | IncuCyte Chemotaxis Software | 2026-07-27 09:35:37 | 11 | |||||||||
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REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | web application, software resource | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-07-27 09:31:46 | 20615 | |||||
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Exonic Splicing Enhancer Finder Resource Report Resource Website 50+ mentions |
Exonic Splicing Enhancer Finder (RRID:SCR_002835) | analysis service resource, service resource, data analysis service, production service resource | A web-based analysis service for identifying exonic splicing enhancers in eukaryotic genes. ESEfinder accept sequences in the FASTA format. A typical mammalian gene is composed of several relatively short exons that are interrupted by much longer introns. To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently, in a process that requires the coordinated action of five small nuclear (sn)RNAs (U1, U2, U4, U5 and U6) and more than 60 polypeptides. The inaccurate recognition of exon/intron boundaries or the failure to remove an intron generates aberrant mRNAs that are either unstable or code for defective or deleterious protein isoforms. Exonic enhancers are thought to serve as binding sites for specific serine/arginine-rich (SR) proteins, a family of structurally related and highly conserved splicing factors characterized by one or two RNA-recognition motifs (RRM) and by a distinctive C-terminal domain highly enriched in RS dipeptides (the RS domain). The RRMs mediate sequence-specific binding to the RNA, and so determine substrate specificity, whereas the RS domain appears to be involved mainly in protein-protein interactions. SR proteins bound to ESEs can promote exon definition by directly recruiting the splicing machinery through their RS domain and/or by antagonizing the action of nearby silencer elements. Sponsors: ESEfinder is supported by the Cold Spring Harbor Laboratory. | element, enhancer, eukaryotic, exon, exonic, gene, analysis, arginine, boundary, c-terminal, dipeptide, intron, isoform, mammalian, mrna, nuclear, polypeptide, protein, recognition, rna, serine, service, snrna, splice | has parent organization: Cold Spring Harbor Laboratory | Free, Freely available | nif-0000-25204 | SCR_002835 | ESEfinder | 2026-07-27 09:31:38 | 66 | ||||||||
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BiSearch: Primer Design and Search Tool Resource Report Resource Website 50+ mentions |
BiSearch: Primer Design and Search Tool (RRID:SCR_002980) | BiSearch | analysis service resource, service resource, data analysis service, production service resource | BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification. | dna, sequence, primer, design, algorithm, analysis, priming, bisulfite, genome, amplification, in vitro, in silico, amplification, epcr, cytosines | has parent organization: Hungarian Academy of Sciences; Budapest; Hungary | PXE International Inc. GVOP-3.1.1-2004-05-0143/3.0; Boolyai Janos Scholarship ; OTKA T34131; OTKA D42207 |
PMID:17022803 PMID:15653630 |
nif-0000-30170 | SCR_002980 | 2026-07-27 09:31:38 | 50 | |||||||
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Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | analysis service resource, service resource, data analysis service, production service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/, http://www.gepas.org/, http://babelomics3.bioinfo.cipf.es | http://www.babelomics.org | SCR_002969 | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-07-27 09:31:39 | 136 | |||
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TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | analysis service resource, service resource, data analysis service, production service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-07-27 09:32:19 | 5 | ||||||
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GraphWeb Resource Report Resource Website 10+ mentions |
GraphWeb (RRID:SCR_005746) | GraphWeb | analysis service resource, service resource, data analysis service, production service resource | GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool | analysis, biological network, ontology or annotation visualization, protein interaction, gene id conversion, orthology mapping, network visualization, graph clustering, gene ontology, cis-regulatory motif, module, network, pathway, biological pathway, motif, visualization, protein interaction, orthology mapping, network visualization, graph clustering, analysis, statistical analysis, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group |
European Union FP6 ENFIN LSHG-CT-2005-518254; European Union FP6 COBRED LSHB-CT-2007-037730; Estonian Science Foundation ETF7437 |
PMID:18460544 | Open unspecified license - Free for academic use | nlx_149205 | SCR_005746 | 2026-07-27 09:32:21 | 12 | ||||||
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CateGOrizer Resource Report Resource Website 50+ mentions |
CateGOrizer (RRID:SCR_005737) | CateGOrizer | analysis service resource, service resource, data analysis service, production service resource | CateGOrizer takes batch input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool | gene ontology, statistical analysis, slimmer-type tool, go term classification, classification, analysis, go slim |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: NAGRP Bioinformatics Coordination Program |
Free for academic use | nlx_149197 | SCR_005737 | GO Terms Classifications Counter | 2026-07-27 09:32:21 | 81 | |||||||
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Cerebellar Platform Resource Report Resource Website 1+ mentions |
Cerebellar Platform (RRID:SCR_001700) | Cerebellar Platform | software repository, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation. | electrophysiology, function, analysis, cerebellar, data, imaging, mathematical, model, molecular biology, paper, plasticity, program, review, script, structure, theory, book, cerebellum |
is used by: NIF Data Federation is related to: Integrated Software has parent organization: RIKEN Brain Science Institute |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10193 | SCR_001700 | 2026-07-27 09:31:18 | 1 | |||||||
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VectorFriends Resource Report Resource Website |
VectorFriends (RRID:SCR_001230) | VectorFriends | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists. | cloning, isothermal assembly, pcr, primer design, data management, sequence analysis, sequence, analysis, primer, windows, mac os | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02113 | SCR_001230 | 2026-07-27 09:31:09 | 0 | ||||||||
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DEAPdataset Resource Report Resource Website 10+ mentions |
DEAPdataset (RRID:SCR_001586) | DEAPdataset | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 12,2025. Multimodal dataset for emotion analysis using EEG, Physiological and Video Signals of human affective states. The electroencephalogram (EEG) and peripheral physiological signals of 32 participants were recorded as each watched 40 one-minute long excerpts of music videos. Participants rated each video in terms of the levels of arousal, valence, like/dislike, dominance and familiarity. For 22 of the 32 participants, frontal face video was also recorded. A novel method for stimuli selection was used, utilizing retrieval by affective tags from the last.fm website, video highlight detection and an online assessment tool. The dataset is made publicly available and other researchers are encouraged to use it for testing their own affective state estimation methods. | emotion, analysis, eeg, physiological, video, signal, affective state, physiological recording, video recording | has parent organization: Queen Mary University of London; London; United Kingdom | European Community's Seventh Framework Program (FP7/2007-2011) grant agreement 216444; BrainGain Smart Mix Programme ; Swiss National Foundation for Scientific Research ; NCCR Interactive Multimodal Information Management |
THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_153824 | SCR_001586 | DEAP: A Dataset for Emotion Analysis using EEG Physiological and Video Signals, DEAPDataset: A Dataset for Emotion Analysis using EEG Physiological and Video Signals | 2026-07-27 09:31:14 | 17 | ||||||
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BioJupies Resource Report Resource Website 50+ mentions |
BioJupies (RRID:SCR_016346) | web application, software resource | Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text. | automatically, generate, RNAseq, data, analysis, notebook, create, visualize, report, custom, raw, processed, user, interface | is affiliated with: Icahn School of Medicine at Mount Sinai; New York; USA | Free, Available for download, Freely available | SCR_016346 | 2026-07-27 09:35:16 | 65 |
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