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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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COsleep Resource Report Resource Website 1+ mentions |
COsleep (RRID:SCR_017053) | cosleep | software application, data processing software, data analysis software, software resource | Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton. | SpiSOP, OpenBCI, sleep, EEG, analysis, electroencephalogram, electrical, activity, brain, wave, pattern, disorder |
is related to: SpiSOP is related to: Python Programming Language |
Free, Available for download, Freely available | http://www.spisop.org/cosleep | SCR_017053 | Closed- and Open-loop Sleep Stimulations with Auditory Stimuli, Closed and Open loop sleep | 2026-02-15 09:21:54 | 1 | |||||||
|
affydata Resource Report Resource Website |
affydata (RRID:SCR_016976) | AffyData | software application, data processing software, software resource, data or information resource, data analysis software | Software R package for analysis of Affymetrix Data. Contains samples data files of a large size. | analysis, Affymetrix, data, large, dataset, oligonucleotide, array |
is listed by: Bioconductor is related to: affy is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016976 | affydata, Affymetrix Data, Affymetrix Data for Demonstration Purpose | 2026-02-15 09:21:52 | 0 | ||||||||
|
CCPN Analysis Resource Report Resource Website 10+ mentions |
CCPN Analysis (RRID:SCR_016984) | CcpNmr Analysis | software application, data visualization software, data processing software, software resource, data analysis software | Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix. | interactive, NMR, specturm, visualization, resonance, data, analysis |
is related to: University of Cambridge; Cambridge; United Kingdom is related to: Python Programming Language is related to: Collaborative Computing Project for NMR works with: CCPN Data Model works with: CCPN Data Model |
Deutsche Forschungsgemeinschaft ; Biotechnology and Biological Sciences Research Council (UK) |
PMID:21953355 PMID:15815974 |
Public, Available for download, Free of charge for non profit institutions, Tutorial available | SCR_016984 | CcpNmr Analysis, CCPN Analysis v2, CCPN Analysis v3 | 2026-02-15 09:21:57 | 47 | ||||||
|
SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software application, data processing software, data analysis software, software resource | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-02-15 09:22:21 | 25 | ||||||||
|
piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-02-15 09:22:23 | 4 | ||||||||
|
TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features. | Tumor, tumor infiltrating immune cell, immune cell, cell, analysis, cancer cell, cancer type, tumor immunological feature, tumor genomic feature, display | National Natural Science Foundation of China ; NCI CA180980; Dana-Farber Cancer Institute |
PMID:29092952 | Free, Freely available | SCR_018737 | Tumor IMmune Estimation Resource | 2026-02-15 09:22:23 | 2042 | |||||||
|
rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | rVista 2.0 | 2026-02-15 09:22:15 | 30 | ||||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NICHD R01 HD068395; NIMH R21 MH112449; NICHD R21 HD075662; NIDA P30 DA027828; NIAID P30 AI050409; NIAID P30 AI027757; NICHD T32 HD007543 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-02-15 09:22:22 | 7 | ||||||
|
QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | software application, data processing software, software resource, software toolkit, data analysis software | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-02-15 09:22:22 | 26 | ||||||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-15 09:22:25 | 3 | |||||||
|
BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | software application, data visualization software, data processing software, software resource, web application | Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. | Box plot generation, customized box plot, data, plot, analysis |
is listed by: SoftCite is related to: PlotsOfData is related to: vioplot |
Wellcome Trust ; WTCCB ; ERC ; Genome Québec International Recruitment Award |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | 2026-02-15 09:20:56 | 360 | ||||||
|
Template Project Resource Report Resource Website |
Template Project (RRID:SCR_015516) | NIAG | organization portal, project portal, data or information resource, portal | Project to house templates used to build other projects. It is also known as the NeuroImaging and Analysis Group, which employs various physiological, functional and structural neuroimaging methodologies in both research and clinical domains. | template, project template, project-building, neuroimaging, analysis | SCR_015516 | NeuroImaging and Analysis Group | 2026-02-15 09:20:55 | 0 | ||||||||||
|
FiberApp Resource Report Resource Website 10+ mentions |
FiberApp (RRID:SCR_015826) | software application, data processing software, data analysis software, software resource | Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects. | semiflexible polymer, neurodegenerative disease, fiber-like object, topography, tracking, analysis, microscopic image analysis | Swiss National Science Foundation SNF 2-77002-11 | Open source, Available for download | SCR_015826 | FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Biomacromolecules, Filaments, and Fibrous Objects | 2026-02-15 09:21:39 | 27 | |||||||||
|
Genesis Resource Report Resource Website 1000+ mentions |
Genesis (RRID:SCR_015775) | software application, data visualization software, data processing software, software resource, data analysis software | Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. | cluster analysis, microarray data, java, gene expression, visualization, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:11836235 | Free for academic use, Free for non-profits, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux | biotools:genesis_microarray | https://bio.tools/genesis_microarray | SCR_015775 | Genesis: Cluster analysis of microarray data | 2026-02-15 09:20:58 | 1018 | ||||||
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Decision Decoding Toolbox Resource Report Resource Website 1+ mentions |
Decision Decoding Toolbox (RRID:SCR_015978) | DDTBOX | software application, data processing software, software resource, software toolkit, data analysis software | Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB. | erp, event, related, potential, multivariate, analysis, pattern, matlab, mvpa | Free, Available for download | SCR_015978 | The Decision Decoding Toolbox (DDTBOX), DDTBOX: Decision Decoding Toolbox | 2026-02-15 09:21:28 | 3 | |||||||||
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/ https://github.com/avogadro https://bio.tools/avogadro https://sources.debian.org/src/axe-demultiplexer/ |
SCR_015983 | 2026-02-15 09:21:29 | 1965 | ||||||
|
Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT098051; Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis https://sources.debian.org/src/bio-tradis/ |
SCR_015993 | 2026-02-15 09:21:00 | 51 | |||||
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andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | software application, data processing software, algorithm resource, software resource, alignment software, image analysis software | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi https://sources.debian.org/src/andi/ |
SCR_015971 | 2026-02-15 09:21:29 | 41 | ||||||
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eprime-data-clean Resource Report Resource Website |
eprime-data-clean (RRID:SCR_016020) | data management software, software application, data processing software, software resource | Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests. | convert, data, psychology, computerized, experiment, design, collection, analysis, generate, file, errors, conversion, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016020 | 2026-02-15 09:21:00 | 0 | |||||||||
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MicrobeTracker Resource Report Resource Website 100+ mentions |
MicrobeTracker (RRID:SCR_015939) | software application, data processing software, software resource, image analysis software, 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 | 2026-02-15 09:21:42 | 119 |
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