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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Statgraphics Centurion Resource Report Resource Website 1+ mentions |
Statgraphics Centurion (RRID:SCR_015248) | software resource, software application, data analysis software, data processing software, data visualization software | Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers. | statistical analysis software, statistical visualization software, statistical analysis | is listed by: SoftCite | Available for download, Trial available, Available for purchase | SCR_015248 | Statgraphics Centurion XVII | 2026-02-12 09:46:28 | 7 | |||||||||
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MPlus Resource Report Resource Website 500+ mentions |
MPlus (RRID:SCR_015578) | software resource, simulation software, software application, data analysis software, data processing software | Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data. | statistical modeling software, data imaging software, software model, modeling estimator, modeling algorithms | is listed by: SoftCite | Available for purchase, Free demo available, Student pricing is available | SCR_015578 | Mplus Version 8 | 2026-02-12 09:46:34 | 958 | |||||||||
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MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | analysis service resource, data access protocol, software resource, service resource, web service, production service resource, data analysis service | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canadian Institutes for Health Research ; Genome Alberta ; McGill University ; Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-02-12 09:46:10 | 10983 | |||||
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X!Tandem Resource Report Resource Website 10+ mentions |
X!Tandem (RRID:SCR_015645) | software resource, software application, data analysis software, data processing software | Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences. | Search engine, command line tool, matching tandem mass spectra, peptide sequence, protein sequence, protein identification, tandem mass spectrum, xml file, FASEB list |
is listed by: SoftCite is related to: XTandem Parser |
Free, Available for download, Freely available | SCR_018388 | SCR_015645 | 2026-02-12 09:46:18 | 44 | |||||||||
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Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | software resource, simulation software, software application, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-02-12 09:46:22 | 1146 | ||||||
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JASP Resource Report Resource Website 1000+ mentions |
JASP (RRID:SCR_015823) | software resource, software application, data analysis software, data processing software | Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests. | statistical analysis, data analysis, statistical test, frequentist analysis, bayesian analysis, r package |
uses: R Project for Statistical Computing is listed by: SoftCite |
European Research Council | PMID:28685272 | Open source, Free, Available for download, Tutorial available, Runs on Windows, Runs on MAC OS, Runs on Linux | https://github.com/jasp-stats/jasp-desktop | SCR_015823 | 2026-02-12 09:46:21 | 3851 | |||||||
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MCODE Resource Report Resource Website 1000+ mentions |
MCODE (RRID:SCR_015828) | software resource, algorithm resource, software application, data analysis software, data processing software, image analysis software | Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks. | cluster, clustering, graph analysis, network, network topology, interconnectivity | is listed by: SoftCite | Canadian Institutes of Health Research (CIHR) ; Ontario Research and Development Challenge Fund ; MDS-Sciex |
PMID:12525261 PMID:25570063 |
Free, Available for download | http://baderlab.org/Software/MCODE | SCR_015828 | 2026-02-12 09:46:13 | 1150 | |||||||
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Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-02-12 09:46:14 | 81 | ||||||
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EEGLAB Resource Report Resource Website 5000+ mentions |
EEGLAB (RRID:SCR_007292) | EEGLAB | software toolkit, software application, software resource, data processing software | 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 | 2026-02-12 09:44:25 | 6721 | ||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | software application, software resource, data processing software | 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 | 2026-02-12 09:45:20 | 21028 | |||||
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ImageQuant Resource Report Resource Website 5000+ mentions |
ImageQuant (RRID:SCR_014246) | IQTL | image analysis software, software application, software resource, data processing software | 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 | 2026-02-12 09:45:50 | 9230 | ||||||||
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ImageScope Resource Report Resource Website 1000+ mentions |
ImageScope (RRID:SCR_014311) | image analysis software, software application, software resource, data processing software | 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 | 2026-02-12 09:45:57 | 3686 | |||||||||
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ATSAS Resource Report Resource Website 1000+ mentions |
ATSAS (RRID:SCR_015648) | software toolkit, software application, software resource, data processing software | 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 | 2026-02-12 09:46:17 | 1326 | |||||||||
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ProteinLynx Global Server Resource Report Resource Website 100+ mentions |
ProteinLynx Global Server (RRID:SCR_016664) | PLGS | data or information resource, portal, service resource, organization 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 | 2026-02-12 09:46:54 | 197 | |||||||||
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Maestro Resource Report Resource Website 50+ mentions |
Maestro (RRID:SCR_016748) | data or information resource, portal | Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data. | molecular, modeling, environment, computation, data, analyze, organize |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Trial available | SCR_016748 | 2026-02-12 09:46:37 | 79 | ||||||||||
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BlobFinder Resource Report Resource Website 100+ mentions |
BlobFinder (RRID:SCR_015788) | image analysis software, software application, software resource, data processing software | 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 | 2026-02-12 09:46:19 | 129 | ||||||||||
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Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | software application, software resource, data processing software | 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 | 2026-02-12 09:46:55 | 39 | ||||||
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HALO Resource Report Resource Website 50+ mentions |
HALO (RRID:SCR_018350) | HALO | image analysis software, software application, 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 | 2026-02-12 09:46:50 | 77 | ||||||||
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BRASS Resource Report Resource Website 10+ mentions |
BRASS (RRID:SCR_017091) | software resource, software application, data analysis software, data processing software | Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements. | analysis, BAM, file, paired, end, sequencing, determine, rearrangement, breakpoint, assemble |
is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | SCR_017091 | 2026-02-12 09:46:47 | 42 | ||||||||||
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OMTools Resource Report Resource Website 1+ mentions |
OMTools (RRID:SCR_017143) | software toolkit, software resource, alignment software, software application, data analysis software, data processing software, data visualization software, image analysis software | Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles. | optical, mapping, data, processing, analysis, visualization, large, scale, profile, phylogenesis | is listed by: SoftCite | Food and Health Bureau of the Hong Kong Special Administrative Region ; Chinese University of Hong Kong ; HKSAR Research Grants Council ; Lo Kwee-Seong Biomedical Research Fund ; Lee Hysan Foundation |
PMID:28505226 | Free, Available for download, Freely available | SCR_017143 | 2026-02-12 09:46:44 | 2 |
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