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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Elephant Resource Report Resource Website 10+ mentions |
Elephant (RRID:SCR_003833) | Elephant, ElePhAnT | data processing software, data analysis software, software resource, software application, software toolkit | The Electrophysiology Analysis Toolkit (Elephant) is a Python library that provides a modular framework for the analysis of experimental and simulated neuronal activity data, such as spike trains, local field potentials, and intracellular data. Elephant builds on the Neo data model to facilitate usability, to enable interoperability, and to support data from dozens of file formats and network simulation tools. Its analysis functions are continuously validated against reference implementations and reports in the literature. Visualizations of analysis results are made available via the Viziphant companion library. Elephant aims to act as a platform for sharing analysis methods across the field. | electrophysiology, analysis, spike train, local field potential, python |
uses: Neo uses: NumPy uses: SciPy is used by: NetworkUnit has parent organization: NeuralEnsemble |
PMID:31449837 | Free, Available for download, Freely available | nlx_158148 | https://github.com/NeuralEnsemble/elephant | SCR_003833 | Elephant - Electrophysiology Analysis Toolkit, Electrophysiology Analysis Toolkit | 2026-08-04 09:41:00 | 29 | |||||
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Northern Ireland Virtual Tissue Archive Resource Report Resource Website |
Northern Ireland Virtual Tissue Archive (RRID:SCR_004452) | NIVTA | image collection, narrative resource, data or information resource, training material | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability. | clinical trial, biomarker research, tissue microarray, analysis, virtual slide, tissue, archive, data resource | has parent organization: Queens University Belfast; Ireland; United Kingdom | Queen's University Belfast; Ireland; United Kingdom ; Hewlett-Packard |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44619 | SCR_004452 | 2026-08-04 09:41:09 | 0 | |||||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | source code, analysis service resource, storage service resource, software resource, data repository, production service resource, service resource, database, data or information resource | An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket. | stem cell, analysis, cancer stem cell, galaxy, gene, pathway, molecular signature, tissue, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard T.H. Chan School of Public Health |
Cancer | NCI 1RC2CA148222-01 | PMID:22121217 | Free, The community can contribute to this resource | biotools:scde_discovery, nlx_44656 | https://bio.tools/scde_discovery | SCR_004453 | Harvard Stem Cell Discovery Engine, SCDE - Stem Cell Discovery Engine | 2026-08-04 09:41:08 | 57 | |||
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Tree and reticulogram REConstruction Resource Report Resource Website 10+ mentions |
Tree and reticulogram REConstruction (RRID:SCR_004497) | T-REX | data analysis service, analysis service resource, software resource, production service resource, service resource | A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. | phylogenetic tree, analysis, visualization, network, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Quebec in Montreal; Quebec; Canada |
PMID:22675075 | biotools:t-rex, OMICS_04264 | https://bio.tools/t-rex | SCR_004497 | Trex-online | 2026-08-04 09:41:09 | 32 | ||||||
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Mini Analysis Program Resource Report Resource Website 1000+ mentions |
Mini Analysis Program (RRID:SCR_002184) | Mini Analysis | data processing software, software application, software resource, data analysis software | Software tool that detects peaks of any type, any shape, any direction, and any size for neuroscientists who are studying spontaneous activities. Allows detection of virtually any kind of peaks including spontaneous miniature synaptic currents and potentials, action potential spikes, calcium imaging peaks, amperometric peaks, ECG peaks etc. It includes the complex and multiple peak detection algorithm. Has post-detection analyses including essential plots and statistical parameters. Group Analysis provides specialized and detailed analysis options for action potentials, decay fitting, fEPSP/population spikes, amperometry, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Synaptosoft Inc., analysis, peak, spontaneous, activity, synaptic, current, potential, spike, calcium, image, amperometric, ECG, plot, statistical, parameter | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000143, SCR_014441 | SCR_002184 | Mini Analysis, MiniAnalysis | 2026-08-04 09:40:35 | 1137 | ||||||||
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BrainVision Analyzer Resource Report Resource Website 100+ mentions |
BrainVision Analyzer (RRID:SCR_002356) | BVA | data processing software, software application, software resource, data analysis software | Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more. | Brain Products GmbH, neurophysiology, manage, data, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Products |
Commercially available | nlx_155717 | http://www.nitrc.org/projects/bva | SCR_002356 | BrainVision Analyzer, BrainVision Analyzer 2 | 2026-08-04 09:40:37 | 449 | ||||||
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Blind Source Separation and Independent Component Analysis Resource Report Resource Website |
Blind Source Separation and Independent Component Analysis (RRID:SCR_002812) | ICA/BSS, BSS/ICA, | data processing software, source code, data analysis software, software resource, software application | Blind Source Separation and Independent Component Analysis (ICA) algorithms including: An efficient batch algorithm: JADE and Adaptive algorithms: relative gradient algorithms. Associated papers / documentation are included as well as thoughts on Multi-dimensional independent component analysis. * An efficient batch algorithm: JADE - For off-line ICA, an algorithm has been developed based on the (joint) diagonalization of cumulant matrices. "Good" statistical performance is achieved by involving all the cumulants of order 2 and 4 while a fast optimization is obtained by the device of joint diagonalization. JADE has been successfully applied to the processing of real data sets, such as found in mobile telephony and in airport radar as well as to bio-medical signals (ECG, EEG, multi-electrode neural recordings). The strongest point of JADE for applications of ICA is that it works off-the-shelf (no parameter tuning). They advocate using the code provided as a plug-in replacement for PCA (whenever one is willing to investigate if such a replacement is appropriate). The weakest point of the current implementation is that the number of sources (but not of sensors) is limited in practice (by the available memory) to something like 40 or 50 depending on your computer. The JADE algorithm was originally developed to process complex signals, motivated by applications to digital communications. Another implementation is now available which is tuned to process more efficiently real-valued signals. * Adaptive algorithms: relative gradient algorithms - For adaptive source separation, they have developed a class of equivariant algorithms. This means that their performance is independent of the mixing matrix. They are obtained as stochastic relative gradient algorithms. * Multi-dimensional independent component analysis - Performing ICA on ECG signals with the JADE algorithm, it was realized that an interesting extension of the notion of independent component analysis would be to consider an analysis into linear components that would be "as independent as possible" as in ICA, but would be "livin" in subspaces of dimension greater than 1. This could be called "MICA" for Multi-dimensional Independent Component Analysis. | algorithm, analysis, blind, component, separation, signal, source separation, plugin, ecg, eeg, multi-electrode, neural recording, independent component analysis, equivariant algorithm, equivariant, relative gradient, multi-dimensional, matlab, octave, python, c, joint diagonalization, real-valued signal, complex-valued signal | has parent organization: Telecom ParisTech; Paris; France | Free, Freely available, Available for download | nif-0000-24771 | http://www.tsi.enst.fr/icacentral/index.html | SCR_002812 | ICA / BSS, BSS / ICA, BSS and ICA | 2026-08-04 09:40:44 | 0 | ||||||
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GraphPad Prism Resource Report Resource Website 10000+ mentions Rating or validation data |
GraphPad Prism (RRID:SCR_002798) | data processing software, data analysis software, software resource, software application, data visualization software | Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling. | biostatistics, curve, fitting, nonlinear, regression, graphing, statistical, analysis, biology, pharmacology, physiology |
is listed by: SoftCite has parent organization: GraphPad |
Restricted | rid_000081, SCR_015807 | https://www.graphpad.com/features, https://www.graphpad.com/updates/prism-920-release-notes, http://graphpad-prism.software.informer.com/5.0/, https://www.graphpad.com/guides/prism/7/user-guide/index.htm | SCR_002798 | Prism 9.2.0, Graph Pad Prism 7, Graph Pad Prism, GraphPad Prism, Graph pad Prism 5, GraphPad Prism version 9.2.0, Graphpad Prism software, Graph pad Prism 8, Graph pad Prism, Graphpad Prism | 2026-08-04 09:40:44 | 46700 | |||||||
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Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis Resource Report Resource Website 50+ mentions |
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) | CAMERA | data analysis service, portal, analysis service resource, storage service resource, organization portal, production service resource, service resource, data repository, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data. | ecology, energy, environment, gene, analysis, bioinformatics, biological, biology, community, cyberinfrastructure, data, dna, genome, genomics, health care, map, marine, metadata, metagenomic, microbial, microbiology, molecular biology, organism, research, scientific, sequence, sequencing, software, tool, training, viral |
is listed by: OMICtools is related to: VIROME has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | PMID:21045053 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_011924, OMICS_01476, nif-0000-23292 | SCR_002676 | 2026-08-04 09:40:42 | 83 | ||||||
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NUTMEG Resource Report Resource Website 10+ mentions |
NUTMEG (RRID:SCR_002748) | NUTMEG | data processing software, data analysis software, time-series analysis software, signal processing software, software resource, software application, image analysis software, 1d time-series analysis software | Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms. | MEG, EEG, analysis, reconstructing, neural, activation, overlaying, structural, MR, image, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at San Francisco; California; USA |
NIBIB EB022717; NIDCD F31 DC006762; NIDCD R01 DC004855 |
PMID:16012626 | nif-0000-24052 | http://www.nitrc.org/projects/nutmeg, | http://www.radiology.ucsf.edu/research/labs/biomagnetic-imaging/nutmeg | SCR_002748 | Neurodynamic Utility Toolbox for Magnetoencephalography and Electroencephalography | 2026-08-04 09:40:43 | 29 | ||||
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Haploview Resource Report Resource Website 5000+ mentions |
Haploview (RRID:SCR_003076) | Haploview | data processing software, software application, software resource, source code | A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site. | linkage disequilibrium, haplotype, genotype, visualization, analysis, single nucleotide polymorphism, gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is listed by: SoftCite is related to: International HapMap Project is related to: PLINK has parent organization: Broad Institute |
PMID:15297300 PMID:21356869 PMID:20147036 |
Free, Available for download, Freely available | nif-0000-30472 | http://www.broad.mit.edu/personal/jcbarret/haploview/ | SCR_003076 | 2026-08-04 09:40:48 | 6933 | ||||||
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Assembly/Alignment/Annotation of 12 Related Drosophila Species Resource Report Resource Website 10+ mentions |
Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) | portal, data set, topical portal, organism-related portal, data or information resource | A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org. | sequence, annotation, analysis, genome, fruitfly, drosophila, research, comparative, alignment, assembly | has parent organization: Lawrence Berkeley National Laboratory | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30021 | SCR_002921 | AAA: 12 Drosophila Genomes | 2026-08-04 09:40:46 | 35 | ||||||||
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Brainscape Resource Report Resource Website 1+ mentions |
Brainscape (RRID:SCR_002962) | Brainscape | data analysis service, analysis service resource, image repository, storage service resource, production service resource, service resource, data repository, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 23, 2013. Database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain, evaluating neuroanatomical models, and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal. (DICOM data is the image format that can be uploaded.) With Brainscape you can upload, analyze, and share your own data. You can search for, download, and analyze studies in the repository of shared data. The analysis engine works by selecting one or more studies, typing in the coordinates of a brain region of interest, and the seed-region correlation engine computes the correlation structure across the whole brain. (T1, T2 and EPI data are the scan types Brainscape can process.) You decide who can access your data. You can keep it to yourself, share with select colleagues, or share it with everyone. The Brainscape database and analysis tools are open source and freely available. | functional connectivity, fmri bold signal, brain, neuroanatomy, region of interest, resting state, fmri, analysis, processing, dicom, dicom data, t1, t2, epi data, 4-dimensional floating point, raw, statistical comparison, functional topography, neurological, psychiatric, disease, mri, functional, statistical operation, correlation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at San Diego; California; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00501 | SCR_002962 | 2026-08-04 09:40:46 | 2 | ||||||||
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CBU Imaging Wiki Resource Report Resource Website 50+ mentions |
CBU Imaging Wiki (RRID:SCR_003014) | CBU Imaging Wiki | topical portal, portal, data or information resource | Portal where neuroimaging studies are carried out using a Siemens 3T Tim Trio Magnetic Resonance Imaging (or MRI) scanner that is wholly dedicated to studies in Cognitive Neuroscience. From emotions and memories to language and learning, functional neuroimaging is being applied in many different areas of Cognitive Neuroscience. In many cases, this research relies upon support from healthy volunteers although neuroimaging studies are also being conducted in various clinical populations, including depression, anxiety, Parkinson's disease and Alzheimer's disease. | neuroimaging, cognitive neuroscience, mri, scanner, neuroscience, emotion, memory, language, learning, functional neuroimaging, clinical, population, human, analysis, software, disease, brain, imaging, fmri, cognition |
is related to: FslAtlasIntegration has parent organization: MRC Cognition and Brain Sciences Unit is parent organization of: MNI brain and the Talairach atlas is parent organization of: MNI brain and the Talairach atlas |
Depressive Disorder, Anxiety, Parkinson's disease, Alzheimer's disease | MRC | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30307 | SCR_003014 | CBUImaging, MRC CBU Imaging Wiki, MRC Cognition and Brain Sciences Unit Imaging Wiki, Cognition and Brain Sciences Unit Imaging Wiki | 2026-08-04 09:40:47 | 58 | |||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | data processing software, data analysis software, software resource, software application, data visualization software | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba has plug in: iRegulon works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-08-04 09:40:48 | 23431 | |||||
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ATGC: Montpellier bioinformatics platform Resource Report Resource Website 100+ mentions |
ATGC: Montpellier bioinformatics platform (RRID:SCR_002917) | ATGC | portal, topical portal, catalog, database, data or information resource | A bioinformatics platform that is a joint project of several South of France laboratories with available services based on their expertise, issued from their research activities which involve phylogenetics, population genetics, molecular evolution, genome dynamics, comparative and functional genomics, and transcriptome analysis. Most of the software and databases on ATGC are (co)authored by researchers from South of France teams. Some are widely used and highly cited. South of France laboratories: * CRBM (transcriptomes and stem cells). * IBC (computational biology). * MiVEGEC (evolution and phylogeny). * LGDP (plant genomics). * LIRMM (computer science). * South Green (plant genomics). | bioinformatics, genome, genetics, molecular evolution, comparative, functional, dynamics, transcriptome, analysis, database, data analysis service, software resource, data set, high-throughput sequencing, binary, phylogenetics, population genetics, genome dynamics, comparative genomics, functional genomics, transcriptome analysis, molecular, evolution, stem cell, computational biology, plant genomics, FASEB list |
is related to: ReNaBi has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: MPscan |
nif-0000-30044 | SCR_002917 | ATGC - South of France bioinformatics platform | 2026-08-04 09:40:46 | 218 | ||||||||
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BioImage Suite Resource Report Resource Website 50+ mentions |
BioImage Suite (RRID:SCR_002986) | data processing software, software resource, software application, image processing software, image analysis software, data visualization software | Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM. | Analysis, multimodal, multispecies, neuroimaging, data, DTI, fMRI, processing, visualization, registration, surface, editing, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: 3D Slicer has parent organization: Yale University; Connecticut; USA |
NIBIB R03 EB012969; NIBIB R01 EB006494; NIMH MH114805 |
PMID:21249532 | Free, Available for download, Freely available | nif-0000-30179 | https://sources.debian.org/src/bioimagesuite/, http://www.nitrc.org/projects/bioimagesuite, https://medicine.yale.edu/bioimaging/suite/ | http://bioimagesuite.yale.edu/index.aspx | SCR_002986 | Bioimagesuite Web | 2026-08-04 09:40:47 | 54 | ||||
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BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | source code, software resource, software repository, wiki, narrative resource, software toolkit, data or information resource | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl, https://sources.debian.org/src/bioperl/ | SCR_002989 | 2026-08-04 09:40:47 | 402 | |||||
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FieldTrip Resource Report Resource Website 1000+ mentions |
FieldTrip (RRID:SCR_004849) | data processing software, data analysis software, software resource, software application, software toolkit | Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists. | MEG, EEG, iEEG, analysis, data, time, frequency, source, reconstruction, dipole, beamformers, non parametric, statistical, testing |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Connectome Coordination Facility has parent organization: Radboud University; Nijmegen; The Netherlands works with: CoSMoMVPA works with: SleepTrip works with: EEGLAB works with: SPM |
Human Connectome project ; NIH Blueprint for Neuroscience Research ; Netherlands Ministry of Economic Affairs ; Netherlands Ministry of Education Culture and Science |
PMID:21253357 | Free, Available for download, Freely available, Tutorial available | nlx_143928 | http://www.nitrc.org/projects/fieldtrip | SCR_004849 | 2026-08-04 09:41:14 | 3073 | ||||||
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, software resource, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-08-04 09:40:05 | 16 |
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