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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 processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:45:32 | 14 | ||||||||||
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Stem Resource Report Resource Website 1+ mentions |
Stem (RRID:SCR_024499) | data processing software, software application, software resource, data analysis software | 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 | Short Time-series Expression Miner | 2026-08-04 09:45:32 | 5 | ||||||||
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Agilent Seahorse Wave Resource Report Resource Website 10+ mentions |
Agilent Seahorse Wave (RRID:SCR_024491) | data processing software, software application, software resource, data acquisition software | 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 | Seahorse Wave | 2026-08-04 09:45:32 | 18 | ||||||||||
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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 | Local Distance Difference Test | 2026-08-04 09:45:32 | 1 | ||||||||
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RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, software resource, web service | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/, http://www.rnalocate.org/ | SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-08-04 09:45:30 | 12 | ||||||
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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 | 2026-08-04 09:45:33 | 1 | |||||||||
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Mutation Assessor Resource Report Resource Website 100+ mentions |
Mutation Assessor (RRID:SCR_024502) | web application, software resource | 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 | 2026-08-04 09:45:32 | 493 | ||||||||||
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CRISPResso2 Resource Report Resource Website 10+ mentions |
CRISPResso2 (RRID:SCR_024503) | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:45:32 | 44 | ||||||||||
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OpenBUGS Resource Report Resource Website 100+ mentions |
OpenBUGS (RRID:SCR_024488) | data processing software, software application, software resource, data analysis software | 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 | Open Bayesian inference Using Gibbs Sampling | 2026-08-04 09:45:32 | 154 | |||||||||
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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 | 2026-08-04 09:45:34 | 2 | |||||||||
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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 | ModFOLD6, ModFOLD8 | 2026-08-04 09:45:32 | 2 | ||||||||
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MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | data processing software, software application, software resource, image analysis software | 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 | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2026-08-04 09:40:39 | 122 | ||||||
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SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-08-04 09:41:18 | 740 | |||||
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HaploReg Resource Report Resource Website 1000+ mentions |
HaploReg (RRID:SCR_006796) | HaploReg | database, data or information resource | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. | chromatin state, conservation, regulatory motif, alteration, variant, chromatin, motif, annotation, genome, variation, genome-wide association study, refsnp, refseq gene, snp, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Broad Institute |
NHGRI R01-HG004037; NHGRI RC1-HG005334; NSF 0644282 |
PMID:22064851 | biotools:HaploReg, nlx_151407 | http://compbio.mit.edu/HaploReg, https://bio.tools/HaploReg | SCR_006796 | 2026-08-04 09:41:42 | 1004 | ||||||
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MUMmer Resource Report Resource Website 100+ mentions |
MUMmer (RRID:SCR_018171) | data processing software, alignment software, software resource, software application, image analysis software | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-08-04 09:44:17 | 480 | |||||
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ProSAS Resource Report Resource Website 1+ mentions |
ProSAS (RRID:SCR_007876) | ProSAS | database, data or information resource | This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids. |
is listed by: SoftCite has parent organization: Ludwig-Maximilians-University; Munich; Germany |
SCR_007876 | Protein Structure and Alternative Splicing | 2026-08-04 09:41:58 | 1 | ||||||||||
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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 | 2026-08-04 09:41:48 | 6721 | ||||
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ImageQuant Resource Report Resource Website 5000+ mentions |
ImageQuant (RRID:SCR_014246) | IQTL | data processing software, software application, software resource, image analysis 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 | 2026-08-04 09:43:23 | 9230 | ||||||||
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ImageScope Resource Report Resource Website 1000+ mentions |
ImageScope (RRID:SCR_014311) | data processing software, software application, software resource, image analysis 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 | 2026-08-04 09:43:23 | 3686 | |||||||||
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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 | Trimmomatic v 0.32 | 2026-08-04 09:42:52 | 21028 |
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