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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ToposPro Resource Report Resource Website 10+ mentions |
ToposPro (RRID:SCR_024496) | data analysis software, data processing software, software application, software resource | Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters. | geometrical and topological properties analysis, crystals, networks, tilings, periodic structures analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024496 | SciCrunch Registry | 2026-10-24 12:49:42 | 18 | ||||||||||
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Stem Resource Report Resource Website 1+ mentions |
Stem (RRID:SCR_024499) | data analysis software, data processing software, software application, software resource | Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology. | short time series gene expression data analysis, clustering, comparing, visualizing, short time series gene expression data, microarray experiments data, identify temporal expression profiles identify genes associated with expression profiles, compare behavior of genes across multiple conditions, | is listed by: SoftCite | PMID:16597342 | Free, Available for download, Freely available | SCR_024499 | SciCrunch Registry | Short Time-series Expression Miner | 2026-10-24 12:49:41 | 6 | ||||||||
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Agilent Seahorse Wave Resource Report Resource Website 10+ mentions |
Agilent Seahorse Wave (RRID:SCR_024491) | data acquisition software, data processing software, software application, software resource | Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis. | Instrument control, data acquisition, Agilent Seahorse XFe96 analyzer, Agilent Seahorse XFe24 analyzer, predefined assay templates, streamlined experimental design, simplified metabolic analysis, | is listed by: SoftCite | SCR_024491 | SciCrunch Registry | Seahorse Wave | 2026-10-24 12:49:42 | 27 | ||||||||||
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lDDT Resource Report Resource Website 1+ mentions |
lDDT (RRID:SCR_024524) | data access protocol, software resource, web service | Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility. | local superposition free score, comparing protein structures and models, distance difference tests, | is listed by: SoftCite | PMID:23986568 | Free, Freely available | SCR_024524 | SciCrunch Registry | Local Distance Difference Test | 2026-10-24 12:49:42 | 2 | ||||||||
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SimPhy Resource Report Resource Website 1+ mentions |
SimPhy (RRID:SCR_024501) | simulation software, software application, software resource | Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees. | phylogenomic simulation, gene phylogenomic simulation, locus phylogenomic simulation, species trees phylogenomic simulation, | is listed by: SoftCite | PMID:26526427 | Free, Available for download, Freely available | SCR_024501 | SciCrunch Registry | 2026-10-24 12:49:42 | 1 | |||||||||
|
Mutation Assessor Resource Report Resource Website 500+ mentions |
Mutation Assessor (RRID:SCR_024502) | software resource, web application | Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional impact of amino-acid substitutions in proteins prediction, | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_024502 | SciCrunch Registry | 2026-10-24 12:49:42 | 535 | ||||||||||
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CRISPResso2 Resource Report Resource Website 50+ mentions |
CRISPResso2 (RRID:SCR_024503) | data analysis software, data processing software, software application, software resource | Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | sequencing data analysis, genome editing experiments interpretation, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024503 | SciCrunch Registry | 2026-10-24 12:49:41 | 61 | ||||||||||
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OpenBUGS Resource Report Resource Website 100+ mentions |
OpenBUGS (RRID:SCR_024488) | data analysis software, data processing software, software application, software resource | Software for analysing complex statistical models using Markov chain Monte Carlo methods. | analysing complex statistical models, Markov chain Monte Carlo method, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024488 | SciCrunch Registry | Open Bayesian inference Using Gibbs Sampling | 2026-10-24 12:49:41 | 161 | |||||||||
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AutoRT Resource Report Resource Website 1+ mentions |
AutoRT (RRID:SCR_024513) | simulation software, software application, software resource | Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides. | proteogenomics analysis | is listed by: SoftCite | PMID:32273506 | Free, Available for download, Freely available | SCR_024513 | SciCrunch Registry | 2026-10-24 12:49:41 | 3 | |||||||||
|
ModFOLD Resource Report Resource Website 1+ mentions |
ModFOLD (RRID:SCR_024518) | data access protocol, software resource, web service | Web server for the global and local quality estimation of 3D protein models | quality estimation, 3D protein models, | is listed by: SoftCite | PMID:28460136 | Restricted | SCR_024518 | SciCrunch Registry | ModFOLD6, ModFOLD8 | 2026-10-24 12:49:43 | 5 | ||||||||
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Metscape Resource Report Resource Website 100+ mentions |
Metscape (RRID:SCR_014687) | resource, software resource, source code | A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data. | metabolomics, metabolomics tool, visualization, expression profiling, gene, compound, metabolism, human |
is listed by: Metabolomics Workbench is listed by: SoftCite |
NIDDK U24 DK097153; NIDDK P30DK089503 |
PMID:22135418 | Freely available | SCR_014687 | SciCrunch Registry | 2026-10-24 12:49:45 | 154 | ||||||||
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MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | data processing software, image analysis software, software application, software resource | A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. | reusable library, c, file format, fortran, information specification, minc, minc2, magnetic resonance, os independent, perl, sh/bash, unix shell |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite is related to: MINC Example files is related to: Extensible MATLAB Medical image Analysis has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155794 | http://www.nitrc.org/projects/minc | SCR_002391 | SciCrunch Registry | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2026-10-24 12:49:48 | 126 | ||||||
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EEGLAB Resource Report Resource Website 5000+ mentions |
EEGLAB (RRID:SCR_007292) | EEGLAB | data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | 2026-10-24 12:49:53 | 7215 | ||||
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Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | data processing software, software application, 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 | SciCrunch Registry | Trimmomatic v 0.32 | 2026-10-24 12:49:57 | 23444 | |||||
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ImageQuant Resource Report Resource Website 5000+ mentions |
ImageQuant (RRID:SCR_014246) | IQTL | data processing software, image analysis software, software application, 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 | SciCrunch Registry | ImageQuant TL | 2026-10-24 12:49:58 | 9231 | ||||||||
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ImageScope Resource Report Resource Website 1000+ mentions |
ImageScope (RRID:SCR_014311) | data processing software, image analysis software, software application, 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 | SciCrunch Registry | 2026-10-24 12:49:58 | 3691 | |||||||||
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ATSAS Resource Report Resource Website 1000+ mentions |
ATSAS (RRID:SCR_015648) | data processing software, software application, software resource, software toolkit | 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 is related to: DAMMIF |
PMID:28808438 | SCR_015648 | SciCrunch Registry | Data Analysis Software ATSAS | 2026-10-24 12:50:00 | 1377 | |||||||||
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ProteinLynx Global Server Resource Report Resource Website 100+ mentions |
ProteinLynx Global Server (RRID:SCR_016664) | PLGS | data or information resource, organization portal, portal, service resource | 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 | SciCrunch Registry | ProteinLynx Global SERVER™ (PLGS), ProteinLynx Global Server, PLGS, ProteinLynx Global Server (PLGS), Protein Lynx Global Server 2.4, Protein Lynx Global Server | 2026-10-24 12:50:01 | 215 | |||||||||
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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 | SciCrunch Registry | 2026-10-24 12:50:01 | 88 | ||||||||||
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BlobFinder Resource Report Resource Website 100+ mentions |
BlobFinder (RRID:SCR_015788) | data processing software, image analysis software, software application, 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 | SciCrunch Registry | 2026-10-24 12:50:00 | 129 |
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