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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Transcriptomics Explorer Resource Report Resource Website 50+ mentions |
Transcriptomics Explorer (RRID:SCR_017567) | data visualization software, data processing software, data analysis software, service resource, software application, software resource | Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus. | Visualize, analyze, transcriptomic, data, cell, type, mouse, human, Allen, database, multiple, cortical, area, cortex, hippocampus | works with: Allen Brain Atlas | Free, Freely available | https://celltypes.brain-map.org/rnaseq/human/cortex https://celltypes.brain-map.org/rnaseq/mouse/cortex-and-hippocampus |
SCR_017567 | 2026-02-13 10:57:59 | 78 | |||||||||
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Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | data analysis software, software resource, data processing software, software application | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-02-13 10:57:59 | 1 | |||||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | ontology, data analysis service, analysis service resource, data or information resource, production service resource, service resource, controlled vocabulary | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-02-13 10:58:01 | 134 | |||||||
|
Project DARE Resource Report Resource Website |
Project DARE (RRID:SCR_017538) | DARE | portal, consortium, data or information resource, organization portal, project portal | EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously. | European Union, infrastructure, workflow, connectivity, layer, methodology, integrated, data, Agile | European Union | SCR_017538 | project-dare, Delivering Agile Research Excellence on European e-Infrastructures | 2026-02-13 10:57:57 | 0 | |||||||||
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STRENDA Resource Report Resource Website 1+ mentions |
STRENDA (RRID:SCR_017422) | STRENDA | data repository, storage service resource, data or information resource, service resource, database | Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal. | Storage, Beilstein Institut, functional, enzymology, data, complition, validation, dataset, guideline, standard, reporting |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FigShare |
Restricted | DOI:10.22011, DOI:10.17616/R3536N, DOI:10.25504/FAIRsharing.ekj9zx, r3d100012329 | http://www.strenda-db.org/ https://doi.org/10.17616/R3536N https://doi.org/10.17616/r3536n https://doi.org/10.22011/ https://dx.doi.org/10.22011/ https://fairsharing.org/10.25504/FAIRsharing.ekj9zx https://doi.org/10.17616/R3536N |
SCR_017422 | , Standards for Reporting Enzymology Data, Beilstein-Institut, STRENDA | 2026-02-13 10:57:57 | 3 | ||||||
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SICAS Medical Image Repository Resource Report Resource Website 1+ mentions |
SICAS Medical Image Repository (RRID:SCR_017420) | data repository, storage service resource, service resource | Medical image repository to store medical research data. | Medical, image, repository, store, data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Freely available | r3d100011560 | https://doi.org/10.17616/R3HP8C | SCR_017420 | Medical Image Repository, SICAS, SICAS Medical Image Repository | 2026-02-13 10:57:59 | 5 | |||||||
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TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data processing software, data analysis software, software toolkit, software application, software resource | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | EU Seventh Framework Programme ; ERC Grant |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-02-13 10:57:58 | 152 | ||||||
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European Variation Archive (EVA) Resource Report Resource Website 50+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | data repository, storage service resource, data or information resource, service resource, database | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | EVA, European Variation Archive | 2026-02-13 10:57:56 | 89 | ||||||
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Single Cell Developmental Database Resource Report Resource Website 1+ mentions |
Single Cell Developmental Database (RRID:SCR_017546) | SCDevDB | data repository, storage service resource, data set, data or information resource, service resource, database | Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes. | Single, cell, gene, expression, profile, human, development, process, data | RGC General Research Fund ; GRF Research Project |
DOI:10.3389/fgene.2019.00903 | Free, Available for download, Freely available | SCR_017546 | Single-Cell Developmental Database | 2026-02-13 10:57:57 | 2 | |||||||
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Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | data processing software, data analysis software, software toolkit, software application, software resource | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | 2026-02-13 10:58:01 | 0 | |||||||||||
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Morpheus by Broad Institute Resource Report Resource Website 1000+ mentions |
Morpheus by Broad Institute (RRID:SCR_017386) | data visualization software, data processing software, data analysis software, service resource, software application, software resource | Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis. | Matrix, visualization, analysis, heatmap, input, data, Java | has parent organization: Broad Institute | Free, Available for download, Freely available | https://github.com/cmap/morpheus.js | SCR_017386 | 2026-02-13 10:57:57 | 1704 | |||||||||
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CLC Genomics Server Resource Report Resource Website 10+ mentions |
CLC Genomics Server (RRID:SCR_017396) | data analysis software, software resource, data processing software, software application | Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler. | high, throughput, sequencing, analysis, data | works with: CLC Genomics Workbench | Restricted | SCR_017396 | 2026-02-13 10:57:59 | 18 | ||||||||||
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GeneLab Resource Report Resource Website 10+ mentions |
GeneLab (RRID:SCR_017658) | GLDS | data repository, storage service resource, data or information resource, service resource, database | Omics database for spaceflight experiments. Interactive, open access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Enables exploration of molecular network responses of terrestrial biology to space environment. Contains curated omics data, metadata and radiation dosimetry for model organisms. Supports standard guidelines for submission of datasets, MIAME for microarray, ENCODE Consortium Guidelines for RNA-seq and MIAPE Guidelines for proteomics. | Omics, spaceflight, experiment, data, system, bioinformatic, repository, terrestrial, biology, space, radiation, dosimetry, model, organism, standard, guideline, submission, dataset |
uses: MIAME is related to: NASA Science |
Space Life and Physical Sciences Division at NASA Headquarters | PMID:30329036 | r3d100013680 | https://www.nasa.gov/centers-and-facilities/ames/what-is-nasas-genelab/ https://doi.org/10.17616/R31NJN1S |
SCR_017658 | GeneLab Data System | 2026-02-13 10:58:02 | 30 | |||||
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LAN toolbox Resource Report Resource Website 1+ mentions |
LAN toolbox (RRID:SCR_017629) | LANtoolbox | data processing software, data analysis software, software toolkit, time-series analysis software, software application, software resource, 1d time-series analysis software | Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB. | Neuroscientist, data, EEG, experimental, analysis, code, script | is related to: MATLAB | Free, Available for download, Freely available | SCR_017629 | Laboratory of Analysis in Neurosciences Toolbox, EEG Toolbox | 2026-02-13 10:57:59 | 2 | ||||||||
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Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | software resource, workflow software, data processing software, software application | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 81573023 ; National Key Research and Development Program 2017YFC0908500 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-02-13 10:58:07 | 2 | |||||
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syGlass Resource Report Resource Website 10+ mentions |
syGlass (RRID:SCR_017961) | data visualization software, data processing software, data analysis software, software application, software resource | Software visualization tool for direct volume rendering with no segmentation required. Enables users to view, annotate and analyze 3D data in VR. Data visualization and annotation system that allows rendering of large, volumetric data in its true, three- or four-dimensional form. | Direct, volume, rendering, no segmentation, view, analyze, annotate, 3D, data, large, volumetric, IstoVisio, Inc | Commercially available | SCR_017961 | 2026-02-13 10:58:06 | 16 | |||||||||||
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Adobe Photoshop Lightroom Resource Report Resource Website 1+ mentions |
Adobe Photoshop Lightroom (RRID:SCR_018012) | image processing software, software resource, data processing software, software application | Camera raw data processing software. Cloud-based service to edit, organize, store, and share photos across any device. | Data, processing, editing, organizing, storing, sharing, photograph, image | is related to: Adobe Photoshop | Restricted | SCR_018012 | 2026-02-13 10:58:06 | 3 | ||||||||||
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ISB Cancer Genomics Cloud Resource Report Resource Website 1+ mentions |
ISB Cancer Genomics Cloud (RRID:SCR_017681) | ISB-CGC | data repository, storage service resource, web application, service resource, software resource | Web tool as flexible cloud-based platform for cancer genomics research. Platform that serves as large-scale repository and provides computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB-CGC is providing access to TCGA data and computation on Google Cloud Platform. | Cancer, genomics, repository, data | National Cancer Institute ; National Institutes of Health |
PMID:29092928 | Restricted | SCR_017681 | ISB Cancer Genomics Cloud, Institute for Systems Biology Cancer Genomics Cloud | 2026-02-13 10:58:08 | 9 | |||||||
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SonarCloud Vulnerable Code Prospector for C Resource Report Resource Website |
SonarCloud Vulnerable Code Prospector for C (RRID:SCR_018011) | SVCP4C | data repository, storage service resource, data set, data or information resource, service resource | Software tool to collect vulnerable source code from open-source repositories linked to SonarCloud. Dataset repository with tagged files with BufferOverflow features associated to source code repositories publicly available. | Repository, SonarCloud, data, dataset, BufferOverflow | DOI:10.3390/app10041270 | Free, Available for download, Freely available | SCR_018011 | SonarCloud Vulnerable Code Prospector for C, SVCP4CDataset | 2026-02-13 10:58:06 | 0 | ||||||||
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GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | data analysis software, software resource, data processing software, software application | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-02-13 10:58:00 | 3 |
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