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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EEGLAB Resource Report Resource Website 5000+ mentions |
EEGLAB (RRID:SCR_007292) | EEGLAB | software application, data processing software, software toolkit, software resource | Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. First developed on Matlab 5.3 under Linux, EEGLAB runs on Matlab v5 and higher under Linux, Unix, Windows, and Mac OS X (Matlab 7+ recommended). EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users'' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB ''datasets'' and/or across a collection of datasets brought together in an EEGLAB ''studyset.'' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data. For creative research programmers and methods developers, EEGLAB offers an extensible, open-source platform through which they can share new methods with the world research community by publishing EEGLAB ''plug-in'' functions that appear automatically in the EEGLAB menu of users who download them. For example, novel EEGLAB plug-ins might be built and released to ''pick peaks'' in ERP or time/frequency results, or to perform specialized import/export, data visualization, or inverse source modeling of EEG, MEG, and/or ECOG data. EEGLAB Features * Graphic user interface * Multiformat data importing * High-density data scrolling * Defined EEG data structure * Open source plug-in facility * Interactive plotting functions * Semi-automated artifact removal * ICA & time/frequency transforms * Many advanced plug-in toolboxes * Event & channel location handling * Forward/inverse head/source modeling | visualization, eeg modeling, independent component analysis, meg modeling, eeg, erp, spectral decomposition, single-trial, matlab, meg, electrophysiology, format conversion, source separation analysis, fourier time-domain analysis, spectral analysis, temporal wavelet analysis, anova, event related potential, three dimensional display, two dimensional display |
uses: ERPwavelab is used by: PeriodAmplitudeAnalysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: SoftCite is related to: Neural Maestro is related to: Measure Projection Toolbox is related to: NFT is related to: Source Information Flow Toolbox is related to: HeadIT is related to: BCILAB is related to: EEGVIS is related to: EYE-EEG (combined eye-tracking & EEG) is related to: Libeep EEGLAB plugin is related to: The Bergen fMRI Toolbox Plugin for EEGLab is related to: BVA import/export EEGLAB plugin has parent organization: Swartz Center for Computational Neuroscience has plug in: Dusk2Dawn works with: FieldTrip |
NINDS | PMID:15102499 | Free, Available for download, Freely available | nif-0000-00076 | https://eeglab.org/others/EEGLAB_References.html | http://www.nitrc.org/projects/incf_eeglab/, http://sccn.ucsd.edu/eeglab/index.html | SCR_007292 | 2026-02-15 09:19:23 | 6721 | ||||
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ImageQuant Resource Report Resource Website 5000+ mentions |
ImageQuant (RRID:SCR_014246) | IQTL | software application, image analysis software, data processing software, software resource | Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automatic image analysis, general image analysis, image analysis software |
is listed by: SoftCite has parent organization: GE Healthcare |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014246 | ImageQuant TL | 2026-02-15 09:20:53 | 9230 | ||||||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | software application, data processing software, software resource | Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows. | trimming, task, paired, end, single, data, next, generation, sequencing, filtering, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill |
BLE/BMELV Verbundprojekt ; BMBF |
PMID:24695404 DOI:10.1093/bioinformatics/btu170 |
biotools:trimmomatic, OMICS_01097 | https://omictools.com/trimmomatic-tool https://bio.tools/trimmomatic https://sources.debian.org/src/trimmomatic/ |
SCR_011848 | Trimmomatic v 0.32 | 2026-02-15 09:20:27 | 21028 | |||||
|
ProteinLynx Global Server Resource Report Resource Website 100+ mentions |
ProteinLynx Global Server (RRID:SCR_016664) | PLGS | organization portal, data or information resource, service resource, portal | Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems. | Waters Corporation, quantitative, qualitative, proteomics, research, system | is listed by: SoftCite | SCR_016664 | ProteinLynx Global SERVER™ (PLGS), ProteinLynx Global Server, PLGS, ProteinLynx Global Server (PLGS), Protein Lynx Global Server 2.4, Protein Lynx Global Server | 2026-02-15 09:21:47 | 197 | |||||||||
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BlobFinder Resource Report Resource Website 100+ mentions |
BlobFinder (RRID:SCR_015788) | software application, image analysis software, data processing software, software resource | Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell. | fluorescence, microscopy, average count analysis, single cell analysis, cell calculation |
is listed by: SoftCite has parent organization: Uppsala University; Uppsala; Sweden |
Free, Available for download, Runs on Windows, Tutorial available | SCR_015788 | 2026-02-15 09:21:24 | 129 | ||||||||||
|
ImageScope Resource Report Resource Website 1000+ mentions |
ImageScope (RRID:SCR_014311) | software application, image analysis software, data processing software, software resource | Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | slide image modification, viewing program |
is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | http://www.leicabiosystems.com/digital-pathology/digital-pathology-management/imagescope/ | SCR_014311 | 2026-02-15 09:20:55 | 3686 | |||||||||
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ATSAS Resource Report Resource Website 1000+ mentions |
ATSAS (RRID:SCR_015648) | software application, data processing software, software toolkit, software resource | Software toolkit for small-angle scattering data analysis from biological macromolecules. | macromolecule, small-angle scattering, ab initio method, rigid body modeling, pbd oriented tool, mixture, flexible system | is listed by: SoftCite | PMID:28808438 | SCR_015648 | Data Analysis Software ATSAS | 2026-02-15 09:21:22 | 1326 | |||||||||
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Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | software application, data processing software, software resource | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-02-15 09:21:48 | 39 | ||||||
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Vmatch Resource Report Resource Website 10+ mentions |
Vmatch (RRID:SCR_018968) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch https://sources.debian.org/src/vmatch/ |
SCR_018968 | 2026-02-15 09:22:20 | 35 | ||||||||
|
Leica QWin Resource Report Resource Website 1+ mentions |
Leica QWin (RRID:SCR_018940) | software application, image processing software, data processing software, software resource, image analysis software | Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional. | Leica, microscope, digital camera, image analysis, image processing, quantitative microscopy | is listed by: SoftCite | Restricted | http://www.mcbainsystems.com/pdf/Leica_QWin.pdf | SCR_018940 | 2026-02-15 09:22:20 | 4 | |||||||||
|
PAST Resource Report Resource Website 100+ mentions |
PAST (RRID:SCR_019129) | software application, data processing software, data analysis software, software resource | Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy. | Paleontological statistics, data analysis, data manipulation function, data plotting, multivariate statistics, ecological analysis, spatial analysis, morphometrics, stratography | is listed by: SoftCite | Free, Available for download, Freely available | SCR_019129 | PAST 4.03, PAleontological STatistics | 2026-02-15 09:21:48 | 123 | |||||||||
|
MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | software application, data processing software, software resource, data analytics software, data analysis software | Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. | Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide |
uses: Mascot is listed by: SoftCite |
Free, Available for download | http://msquant.alwaysdata.net/ | SCR_019206 | 2026-02-15 09:22:28 | 4 | |||||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | software application, data processing software, data analysis software, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-02-15 09:22:28 | 2638 | ||||||
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V3D Resource Report Resource Website 1+ mentions |
V3D (RRID:SCR_008646) | V3D | software application, data visualization software, data processing software, software resource, d visualization software, segmentation software, image analysis software | V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily. | 3d, annotation, bioimage, brain, cell, development, informatics, neuron, registration, segmentation, software, tracing, visual, visualization, image |
is listed by: SoftCite has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | nif-0000-32975 | SCR_008646 | V3D: A Swiss army knife for bioimage visualization & analysis | 2026-02-15 09:19:53 | 3 | ||||||
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FASTA Resource Report Resource Website 500+ mentions |
FASTA (RRID:SCR_011819) | FASTA | software application, sequence analysis software, data processing software, software resource, data analysis software | Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. | sequence, alignment, DNA, protein, similarity, searching |
is listed by: OMICtools is listed by: SoftCite has parent organization: European Bioinformatics Institute |
Free, Freely available | OMICS_00994 | SCR_011819 | Federal Acquisition STreamlining Act | 2026-02-15 09:20:24 | 845 | |||||||
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CMap Resource Report Resource Website 100+ mentions |
CMap (RRID:SCR_016204) | data set, database, software resource, web application, data or information resource | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-02-15 09:21:50 | 483 | |||||||
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DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software tool, software application, data processing software, software resource, data analysis software | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2 https://bio.tools/deseq2 |
SCR_015687 | 2026-02-15 09:21:36 | 43994 | |||||||
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Pipeline Pilot Resource Report Resource Website 100+ mentions |
Pipeline Pilot (RRID:SCR_014917) | software application, data processing software, data analysis software, software resource | Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results. | automation, accessing, analysis, analyzing, scientific data, aggregation. aggregate, research, scientific | is listed by: SoftCite | Commercial | SCR_014917 | 2026-02-15 09:21:02 | 352 | ||||||||||
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pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | software application, data processing software, software resource, data acquisition software, image acquisition software, software toolkit | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf https://bio.tools/pheatmap https://sources.debian.org/src/r-cran-pheatmap/ |
SCR_016418 | pretty heatmap | 2026-02-15 09:21:40 | 1068 | ||||||
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Protein preparation Wizard Resource Report Resource Website 10+ mentions |
Protein preparation Wizard (RRID:SCR_016749) | software application, simulation software, software resource | Software tool for correcting common structural problems and creating reliable, all atom protein models. | correcting, structural, problem, atom, protein, model, virtual, docking, method |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Training available | SCR_016749 | protein preparation wizard, Protein Preparation Wizard | 2026-02-15 09:21:10 | 12 |
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