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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | software application, data processing software, data analysis software, software resource | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | NIDDK R24 DK096518; NHLBI R24 HL123482; NIDDK R01 DK115791; Fraternal Order of Eagles Diabetes Research Center ; University of Iowa Center for Gene Therapy ; Carver Chair in Molecular Medicine ; NIGMS T32 GM082729 |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-02-15 09:21:57 | 5 | |||||||||
|
sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | software application, data processing software, data analysis software, software resource | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NIDDK R01 DK094699; NHGRI R01 HG006129 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth https://bio.tools/sleuth https://bio.tools/sleuth |
SCR_016883 | 2026-02-15 09:21:55 | 24 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | software application, data processing software, data analysis software, software resource | Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. | multivariate, analysis, feature, selection, omics, data, visualization, regression, classification, variable, exceedes, number, sample, multicollinearity, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | BioTools:ropls, biotools:ropls | https://bio.tools/ropls https://bio.tools/ropls https://bio.tools/ropls |
SCR_016888 | R Orthogonal Partial Least Squares | 2026-02-15 09:21:11 | 12 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | software application, data processing software, data analysis software, software resource | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | 2026-02-15 09:21:55 | 354 | |||||||
|
Profinder Resource Report Resource Website 10+ mentions |
Profinder (RRID:SCR_017026) | software application, data processing software, data analysis software, software resource | Software tool as fast, batch processing feature extraction software for differential analysis that supports data from Agilent GC/MSD, GC/Q-TOF, LC/TOF and LC/Q-TOF instruments. Speeds up differential and flux analysis workflows using intuitive user interface. Used to analyze raw mass spectrometry data, choose peaks. | fast, batch, processing, feature, extraction, software, differential, analysis, Agilent, instrument, support, raw, mass, spectrometry, data | Commercially available | SCR_017026 | Profinder 8 | 2026-02-15 09:21:54 | 17 | ||||||||||
|
TransRate Resource Report Resource Website 10+ mentions |
TransRate (RRID:SCR_017034) | software application, data processing software, data analysis software, software resource | Open source software tool for de novo transcriptome assembly reference free quality analysis. Used to examine assembly in detail and compare it to sequencing reads, reporting quality scores for contigs and assemblies to allow to choose between assemblers and parameters, filter out bad contigs from an assembly, and help decide when to stop trying to improve assembly. | de novo, transcriptome, assembly, reference, free, quality, analysis, sequencing, read, contig, parameter | Millennium Seed Bank ; Royal Society University Research ; BBSRC ; European Union Horizon 2020 research and innovation program ; Bill & Melinda Gates Foundation |
PMID:27252236 | Free, Available for download, Freely available | https://github.com/Blahah/transrate | SCR_017034 | 2026-02-15 09:21:54 | 34 | ||||||||
|
IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | software application, data processing software, data analysis software, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-02-15 09:22:18 | 3 | ||||||
|
TwoSampleMR Resource Report Resource Website 500+ mentions |
TwoSampleMR (RRID:SCR_019010) | software application, data processing software, data analysis software, software resource | Software R package for performing Mendelian randomization using genome wide association study summary data. | GWAS data, genome wide associated study data, genome data, Mendelian randomization, analysis | PMID:29846171 | Free, Available for download, Freely available | SCR_019010 | 2026-02-15 09:22:25 | 597 | ||||||||||
|
RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | software application, data processing software, data analysis software, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIGMS R01 GM104962; Berlin Institute for Medical Systems Biology |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html https://bio.tools/ribotaper |
SCR_018880 | 2026-02-15 09:21:43 | 8 | ||||||
|
MRTool Resource Report Resource Website 1+ mentions |
MRTool (RRID:SCR_015956) | data or information resource, topical portal, portal | Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. | brain, imaging, neuroimaging, analysis, magnetic, resonance, mr | requires: SPM | DOI:10.1007/s12021-018-9355-3 | Free, Available for download, Runs on MAC OS, Runs on Windows | SCR_015956 | 2026-02-15 09:21:00 | 8 | |||||||||
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Pattern Component Modelling Toolbox Resource Report Resource Website 1+ mentions |
Pattern Component Modelling Toolbox (RRID:SCR_015891) | PCM | software application, data processing software, data analysis software, software resource | Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model. | bayesian, representational, model, motor, abstract, visual, encoding, neural, imaging, activity, pattern, analysis, voxel | James McDonnell Foundation ; NSERC RGPIN-2016-04890; JSPS 15J03233 |
PMID:28843540 | Free, Available for download | SCR_015891 | Pattern component modeling (PCM), PCM Toolbox, Pattern Component Modeling toolbox for multivariate analysis | 2026-02-15 09:21:28 | 2 | |||||||
|
Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | software application, data processing software, data analysis software, software resource | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | GNU Datamash | 2026-02-15 09:21:46 | 2 | |||||||
|
jamovi Resource Report Resource Website 1000+ mentions |
jamovi (RRID:SCR_016142) | software application, data processing software, data analysis software, software resource | Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience. | spreadsheet, r, statistic, methodology, r, package, analysis | Free, Available for download | SCR_016142 | the jamovi project | 2026-02-15 09:21:32 | 2851 | ||||||||||
|
FITMASTER Resource Report Resource Website 50+ mentions |
FITMASTER (RRID:SCR_016233) | software application, data processing software, data analysis software, software resource | Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series. | electrophysiology, analysis, fitting, statistic, polynomial, exponential, gaussian, boltzmann, formalism, voltage, current | Free, Available for download, Tutorial available, Demo available | SCR_016233 | HEKA FITMASTER | 2026-02-15 09:21:03 | 97 | ||||||||||
|
Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | software application, data processing software, data analysis software, software resource | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-02-15 09:21:31 | 15 | |||||||
|
Easy fMRI Resource Report Resource Website 1+ mentions |
Easy fMRI (RRID:SCR_016392) | software application, data processing software, data analysis software, software resource | Software that employs machine learning techniques and high-performance computing for analyzing task-based fMRI datasets. It applies Feature Analysis, Hyperalignment, Multi-voxel Pattern Analysis (MVPA), Representational Similarity Analysis (RSA), and more. | fmri, imaging, neuroimaging, analysis, fsl, scikit-learn, tensorflow, suma | Open source, Free, Available for download | https://sourceforge.net/projects/easyfmri/files/ https://github.com/easyfmri/easyfmri |
SCR_016392 | easyfMRI | 2026-02-15 09:21:38 | 2 | |||||||||
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ErmineJ Resource Report Resource Website 50+ mentions |
ErmineJ (RRID:SCR_006450) | ermineJ | software application, data processing software, data analysis software, software resource | Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | microarray, gene ontology, analysis, high-throughput, gene, gene expression, statistical analysis, term enrichment, genome |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of British Columbia; British Columbia; Canada has parent organization: Columbia University; New York; USA |
PMID:16280084 | Free for academic use | nif-0000-07758 | SCR_006450 | ermineJ: Gene Ontology analysis for high-throughput data | 2026-02-15 09:19:16 | 50 | ||||||
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FEI Helios Nanolab 600i DualBeam Resource Report Resource Website |
FEI Helios Nanolab 600i DualBeam (RRID:SCR_027033) | instrument resource | Scanning Electron Microscope advanced DualBeam for ultra-high resolution imaging, analysis and fabrication at the nanoscale. Helios NanoLab 600i builds on the success of FEI’s winning DualBeam series offering advances in ion beam, electron beam, patterning and range of features to make milling, imaging, analysis and sample preparation down to nanoscale. | Scanning Electron Microscope, imaging, analysis, nanoscale, microscope, electron microscope, | Model_Number_Helios_NanoLab_600i | SCR_027033 | FEI Helios NanoLab 600i DuaBeam, , FEI Helios NanoLab 600i DuaBeam Scanning Electron Microscope, Helios NanoLab 600i | 2026-02-14 02:09:48 | 0 | ||||||||||
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THEA - Tools for High-throughput Experiments Analysis Resource Report Resource Website |
THEA - Tools for High-throughput Experiments Analysis (RRID:SCR_005802) | THEA | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, on documented July 16, 2012. An integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, analysis, ontology, microarray, genomic, annotation, gene ontology, data mining, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Virtual Biology Lab |
French Ministry of Higher Education and Research ; Bioinformatic Program |
PMID:15130932 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149290 | SCR_005802 | Tools for High-throughput Experiments Analysis | 2026-02-15 09:19:12 | 0 | |||||
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Weighted Gene Co-expression Network Analysis Resource Report Resource Website 1000+ mentions |
Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) | WGCNA | software application, data processing software, data analysis software, software resource | Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, co-expression, analysis, network, bio.tools, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
NCI P50CA092131; NIDA 1R01DA030913-01; NIDCR R01DE019255; NIAID U19 AI063603-01 |
PMID:19114008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31889, biotools:crosslinkwgcna | http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation https://bio.tools/crosslinkwgcna |
SCR_003302 | WGCNA: an R package for weighted correlation network analysis | 2026-02-15 09:18:32 | 1860 |
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