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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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learnMSA Resource Report Resource Website 1+ mentions |
learnMSA (RRID:SCR_022572) | image analysis software, software resource, software application, data processing software, alignment software | Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded. | Multiple sequence alignment, protein sequences, statistical machine learning problem, hidden Markov model | Free, Available for download, Freely available | SCR_022572 | 2026-08-12 10:52:54 | 2 | |||||||||||
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sei Resource Report Resource Website 10+ mentions |
sei (RRID:SCR_022571) | software resource, data access protocol, web service | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | 2026-08-12 10:52:34 | 10 | ||||||||
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pMAT Resource Report Resource Website 1+ mentions |
pMAT (RRID:SCR_022570) | pMAT | data processing software, data analysis software, software resource, software application | Open source software suite for analysis of fiber photometry data. | fiber photometry data analysis, fiber photometry | NIDA DA043572 | PMID:33385438 | SCR_022570 | Photometry Modular Analysis Tool | 2026-08-12 10:52:45 | 8 | ||||||||
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Rphenograph Resource Report Resource Website 10+ mentions |
Rphenograph (RRID:SCR_022603) | data processing software, data analysis software, software resource, software application | Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis. | R, high dimensional single cell data analysis, clustering method |
is related to: Phenograph is related to: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_022603 | 2026-08-12 10:52:45 | 29 | ||||||||||
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IBM SPSS Amos Resource Report Resource Website 10+ mentions |
IBM SPSS Amos (RRID:SCR_022686) | data processing software, data analysis software, software resource, software application | Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance. | regression, factor analysis, correlation and analysis of variance | is related to: IBM SPSS Statistics | Restricted | SCR_022686 | SPSS Amos | 2026-08-12 10:52:46 | 10 | |||||||||
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Enhancing Quality In Preclinical Data Quality System Resource Report Resource Website 1+ mentions |
Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) | data or information resource, narrative resource, standard specification | Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD. | EQIPD certification, guidance on expectations, Enhancing Quality In Preclinical Data, EQIPD consortium, GoEQIPD, reliable preclinical data generation | PMID:34028353 | Free, Freely available | SCR_022729 | EQIPD Quality System | 2026-08-12 10:52:47 | 1 | |||||||||
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Meta Essentials Resource Report Resource Website 10+ mentions |
Meta Essentials (RRID:SCR_022464) | data processing software, data analysis software, software resource, software application | Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more. | meta analysis, relationship between independent and dependent variable analysis | DOI:10.1002/jrsm.1260 | Free, Available for download, Freely available | SCR_022464 | Meta-Essentials | 2026-08-12 10:52:53 | 35 | |||||||||
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Hexamer Additive Linear Resource Report Resource Website 1+ mentions |
Hexamer Additive Linear (RRID:SCR_022581) | HAL | software resource, data access protocol, web service | Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events. | sequence variants on alternative splicing prediction, cassete exon, skipped exon events, changes in alternative 5' splice events, | National Science Foundation Career Award ; Burroughs Wellcome Career Award at the Scientific Interface |
DOI:10.1016/j.cell.2015.09.054 | Free, Freely available | SCR_022581 | 2026-08-12 10:52:54 | 1 | ||||||||
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NetShift Resource Report Resource Website 10+ mentions |
NetShift (RRID:SCR_022733) | software resource, data access protocol, web service | Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets. | Driver microbes, identification of driver nodes, case control association networks, driver nodes between networks | CSIR-National Chemical Laboratory ; Academy of Scientific and Innovative Research |
PMID:30287886 | Free, Freely available | SCR_022733 | Netshif | 2026-08-12 10:52:56 | 10 | ||||||||
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UpSet Resource Report Resource Website 10+ mentions |
UpSet (RRID:SCR_022731) | data visualization software, software application, data processing software, software resource, data analysis software | Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets. | visualize set intersections, matrix layout, intersecting sets, more than three sets quantitative data analysis | Austrian Science Fund ; Air Force Research Laboratory ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | https://github.com/VCG/upset | SCR_022731 | UpSet Plot | 2026-08-12 10:52:37 | 16 | |||||||
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VirtualPlant Resource Report Resource Website 1+ mentions |
VirtualPlant (RRID:SCR_022576) | software resource, data access protocol, web service | Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses. | genomic data integration, support systems biology, genomic data visualization and analysis | NSF DBI 0445666; NSF IOB 0519985; NSF MCB–0209754; FONDECYT ; Grape Genomics ; Millennium Nucleus for Plant Functional Genomics ; NIGMS R01 GM 032877; NIGMS 5F32GM75600 |
PMID:20007449 | Free, Available for download, Freely available | SCR_022576 | VirtualPlant 1.3 | 2026-08-12 10:52:45 | 3 | ||||||||
|
dNdScv Resource Report Resource Website 10+ mentions |
dNdScv (RRID:SCR_023123) | data processing software, data analysis software, software resource, software application | Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies. | quantify dN/dS ratios, missense, nonsense, essential splice mutations, detect cancer driver genes on datasets, whole-exome/genome, targeted sequencing studies, | Free, Freely available, Available for download | SCR_023123 | dN/dScv | 2026-08-12 10:52:59 | 32 | ||||||||||
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BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain Resource Report Resource Website 1+ mentions |
BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain (RRID:SCR_023000) | project portal, portal, data or information resource, organization portal, consortium | Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex. | BRAIN Initiative Cell Census Network, imaging and analysis, construct cell census of human brain, creating cellular census, human cerebral cortex | is organization facet of: BICCN | DOI:10.1101/2021.10.20.464979 | Free, Freely available | SCR_023000 | 2026-08-12 10:52:49 | 2 | |||||||||
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SigProfilerExtractor Resource Report Resource Website 50+ mentions |
SigProfilerExtractor (RRID:SCR_023121) | data processing software, data analysis software, software resource, software application | Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample. | de novo extraction, mutational signatures, data generated in matrix format, operative mutational signatures identification, specific mutation type, cancer sample | is related to: SigProfilerMatrixGenerator | Free, Available for download, Freely available | SCR_023121 | 2026-08-12 10:52:51 | 82 | ||||||||||
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EmaCalc Resource Report Resource Website 1+ mentions |
EmaCalc (RRID:SCR_022943) | data processing software, data analysis software, software resource, software application | Software package in Python for statistical analysis of Ecological Momentary Assessment data. | Ecological Momentary Assessment data analysis, Ecological Momentary Assessment, EMA | Free, Available for download, Freely available | SCR_022943 | 2026-08-12 10:52:40 | 1 | |||||||||||
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MRIQC Resource Report Resource Website 10+ mentions |
MRIQC (RRID:SCR_022942) | data processing software, workflow software, software resource, software application | Software tool as quality assurance workflow for Brain Imaging Data Structure compliant anatomical and functional MRI datasets. Used to extract no-reference image quality metrics from structural and functional magnetic resonance imaging data. | Image quality metrics, brain imaging data structure, quality assurance workflow, BIDS compliant, anatomical and functional MRI datasets, MRI datasets | Laura and John Arnold Foundation ; Swiss National Science Foundation |
PMID:28945803 | Free, Available for download, Freely available | https://github.com/nipreps/mriqc | SCR_022942 | Image Quality in MRI | 2026-08-12 10:52:49 | 26 | |||||||
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CytoTRACE Resource Report Resource Website 100+ mentions |
CytoTRACE (RRID:SCR_022828) | simulation software, software resource, software application | Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data. | differentiation state of cells, single cell RNA sequencing data, predicting differentiation states, scRNA-seq data | NCI R00CA187192; NCI R01CA100225; Stinehart Reed foundation ; Stanford Bio-X Interdisciplinary Initiatives Seed Grants Program ; Virginia and D.K. Ludwig Fund for Cancer Research ; U.S. Department of Defense ; National Science Foundation Graduate Research Fellowship ; Stanford Bio-X Bowes Graduate Student Fellowship ; Stanford Medical Science Training Program |
PMID:31974247 | Free, Freely available | SCR_022828 | Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression | 2026-08-12 10:52:56 | 170 | ||||||||
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Differential Enrichment analysis of Proteomics data Resource Report Resource Website 1+ mentions |
Differential Enrichment analysis of Proteomics data (RRID:SCR_023090) | DEP | data processing software, data analysis software, software resource, software application | Software R package provides integrated analysis workflow for analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. | analysis of mass spectrometry proteomics data, differential protein expression, differential enrichment | PMID:29446774 | Free, Available for download, Freely available | SCR_023090 | Differential Enrichment analysis of Proteomics data | 2026-08-12 10:52:58 | 7 | ||||||||
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Plant mPLoc Resource Report Resource Website 100+ mentions |
Plant mPLoc (RRID:SCR_023014) | software resource, data access protocol, web service | Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization. | Predicting Plant Protein Subcellular Localization, predicting subcellular localization, plant proteins, | National Natural Science Foundation of China ; Science and Technology Commission of Shanghai Municipality ; Shanghai Pujiang Program |
PMID:20596258 | Free, Freely available | SCR_023014 | Plant-mPLoc | 2026-08-12 10:52:58 | 362 | ||||||||
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Multi Loc2 Resource Report Resource Website 1+ mentions |
Multi Loc2 (RRID:SCR_023013) | software resource, data access protocol, web service | Web application for integrating phylogeny and Gene Ontology terms into subcellular protein colalization prediction.Extensive high performance subcellular protein localization prediction system. | subcellular protein localization, prediction system, integrating phylogeny and Gene Ontology terms, subcellular protein colalization prediction | PMID:19723330 | Free, Freely available | SCR_023013 | MultiLoc2 | 2026-08-12 10:52:41 | 5 |
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