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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | data access protocol, software resource, web service | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | METAdata of GEnomics studies on a web based NOTEbook | 2026-02-16 09:49:31 | 1 | ||||||||
|
Stanford University Human Immune Monitoring Center Core Facility Resource Report Resource Website 1+ mentions |
Stanford University Human Immune Monitoring Center Core Facility (RRID:SCR_018266) | HIMC | service resource, core facility, access service resource, data or information resource | Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data. | Immune monitoring serivce, clinical study, translational study, RNA, protein, data, core facility, USEDit, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Stanford University; Stanford; California |
Open | ABRF_399 | https://coremarketplace.org/?FacilityID=399 | SCR_018266 | Stanford University - Human Immune Monitoring Center, Human Immune Monitoring Center (HIMC) | 2026-02-16 09:49:28 | 1 | ||||||
|
ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | service resource, data access protocol, software resource, web service | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R35 GM118078; NIGMS R01 GM061867 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-02-16 09:49:27 | 858 | |||||||
|
Redivis Resource Report Resource Website 1+ mentions |
Redivis (RRID:SCR_023111) | Redivis | software repository, data repository, software resource, service resource, storage service resource | Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data. | Data platform, central hub, discover, access, analyze, data, academic research, hosting datasets, analyzing datasets | is related to: DataCite | Restricted | r3d100014398, 10.57761, SCR_024550 | https://search.datacite.org/repositories/sul.swbvyu https://doi.org/10.57761/ https://dx.doi.org/10.57761 https://doi.org/10.17616/R31NJNLQ |
SCR_023111 | Red Vis | 2026-02-16 09:50:38 | 9 | ||||||
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LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIEHS P30 ES06096; NIEHS U01 ES015675; NHGRI R01 HG003749; NLM R01 LM008106; NIDA U54 DA021519 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-02-16 09:49:29 | 4 | ||||||
|
Islet eQTL Explorer Resource Report Resource Website 1+ mentions |
Islet eQTL Explorer (RRID:SCR_018692) | web service, data access protocol, software resource, service resource, data or information resource | Web tool for exploring variants in islet expression quantitative trait loci. Data is result of collaboration between Michigan University Parker lab, Department of Biostatistics and Center for Statistical Genetics at University of Michigan, National Human Genome Research Institute, Jackson Laboratory for Genomic Medicine, Department of Genetics at University of North Carolina, European Bioinformatics Institute, Department of Preventive Medicine at University of Southern California, and Department of Physiology and Biophysics at University of Southern California. | Exploring variants, islet expression, quantitative trait loci, data, chromatin, chromatin state annotation, gene, footprint, allele | has parent organization: University of Michigan; Ann Arbor; USA | Free, Freely available | SCR_018692 | 2026-02-16 09:49:31 | 1 | ||||||||||
|
ReproMan Resource Report Resource Website 1+ mentions |
ReproMan (RRID:SCR_018468) | software application, software resource, data management software, software toolkit | Software tool to simplify creation and management of computing environments in Neuroimaging. | Simplify computing environment creation, computing environment management, neuroimaging, imaging, data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | ReproMan is under development. | https://github.com/ReproNim/reproman | SCR_018468 | 2026-02-16 09:49:30 | 1 | |||||||||
|
Stanford Medicine Research Data Repository Resource Report Resource Website 100+ mentions |
Stanford Medicine Research Data Repository (RRID:SCR_018686) | STARR | service resource, data repository, storage service resource | Platform developed and operated by Stanford Medicine Research IT team for working with clinical data for research purposes. Permits collection and aggregation of all clinical data generated at Stanford for care purposes, and articulates formal approval process each research project must follow in order to obtain and work with this data for research purpose. Home of stride/web tools for Cohort Discovery and Chart Review. | Clinical data, Stanford data, care purpose, stride web tools, cohort discovery, data | is related to: Stanford University School of Medicine; California; USA | Restricted | https://starr.stanford.edu/team | SCR_018686 | STRIDE-web, STAnford medicine Research data Repository | 2026-02-16 09:49:32 | 213 | |||||||
|
Big Data Processor Resource Report Resource Website 1+ mentions |
Big Data Processor (RRID:SCR_018484) | BDP | software application, data processing software, image processing software, image analysis software, software resource | Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy. | Image, image processor, data processor, data, processing, analysis, image data, microscopy | is a plug in for: Fiji | Free, Available for download, Freely available | https://github.com/embl-cba/fiji-plugin-bigDataProcessor | SCR_018484 | 2026-02-16 09:49:31 | 2 | ||||||||
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reshape Resource Report Resource Website 1+ mentions |
reshape (RRID:SCR_018983) | software application, data processing software, software toolkit, data analysis software, software resource | Software R package for flexibly restructuring and aggregating data. | Data restructuring, data aggregation, flexible data restructuring, data |
is related to: CRAN is related to: reshape2 |
Free, Freely available | SCR_018983 | reshape 0.8 | 2026-02-16 09:49:35 | 4 | |||||||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | data access protocol, data or information resource, web service, software resource | Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes. | Genome annotation, genome visualization, phylogenetic tree, functionally annotated tree, microbial tree of life, taxonomic data, phylogenetic data, functionally annotated data, bacterial genome, archaeal genome, genome distribution, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Ontario Early Researcher award ; NSERC Discovery Grant ; Australian Research Council Laureate Fellowship ; Tier II Canada Research Chair ; Natural Sciences and Engineering Research Council of Canada |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | AnnoTree 1.2 | 2026-02-16 09:49:37 | 22 | |||||
|
SC2diseases Resource Report Resource Website 1+ mentions |
SC2diseases (RRID:SCR_019093) | analysis service resource, database, production service resource, service resource, data or information resource | Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases. | Human disease, single cell transcriptome, data, manually curated data, biomarker | National Natural Science Foundation of China | PMID:33010177 | Free, Freely available | SCR_019093 | 2026-02-16 09:49:40 | 5 | |||||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | software application, data processing software, data visualization software, data analysis software, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-02-16 09:49:35 | 1 | ||||||||
|
Mutation and Patient Database Resource Report Resource Website 1+ mentions |
Mutation and Patient Database (RRID:SCR_018806) | data set, data or information resource, database | Collection of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission. There are two tables for each human NCL disease gene - Patient Datasheets list all published or reported patients and families, and Mutation Datasheets list all published or reported mutations, cross-referenced to patient table. Datasheets are available to view or download as excel files for off-site use to aid local needs or interests. Database follows mutation nomenclature recommendations of Human Genome Variation Society. | Mutation, gene mutation, sequence variations, gene, human NCL disease gene, patient datasheet, mutation datasheet, mutation nomenclature, human genome variation society, data | has parent organization: University College London; London; United Kingdom | Neuronal Ceroid Lipofuscinoses, NCL, Batten disease | Free, Freely available | SCR_018806 | NCL Mutation Database, NCL Mutation and Patient Database | 2026-02-16 09:49:35 | 4 | ||||||||
|
scPancMeta App Resource Report Resource Website 1+ mentions |
scPancMeta App (RRID:SCR_018939) | data or information resource, topical portal, portal | Portal for islet research community. Data for eight scRNA-seq datasets are combined to give consensus overview of islet cell type defining genes. Tools are provided for interacting with and comparing novel genesets generated. | Islet cell, islet genes, data, scRNAseq datasets, islet cell type, gene set generation, gene set comparison, data, islet | is related to: Human Islet Research Network (HIRN) | Restricted | SCR_018939 | 2026-02-16 09:49:34 | 1 | ||||||||||
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CFTR2 Resource Report Resource Website 100+ mentions |
CFTR2 (RRID:SCR_019078) | database, topical portal, portal, data or information resource, disease-related portal | International initiative led by team of researchers and clinicians and supported by the US Cystic Fibrosis Foundation that seeks to provide complete, advanced and expert reviewed functional and clinical information on CFTR mutations. Provides information for patients, researchers, and general public about specific variants. For each variant or variant combination included in database, website will provide information about whether variant or variant combination is CF-causing, and information about sweat chloride, lung function, pancreatic status, and Pseudomonas infection rate in patients in CFTR2 database with this variant or variant combination. | CF gene, cystic fibrosis gene, functional testing, CFTR2 variant, data, CFTR mutations, clinical information, , FASEB list | is related to: Cystic Fibrosis Mutation Database | cystic fibrosis | Free, Freely available | SCR_019078 | Clinical and Functional TRanslation of CFTR, cftr2, Clinical and Functional TRanslation 2 | 2026-02-16 09:49:36 | 127 | ||||||||
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D-EE Resource Report Resource Website 1+ mentions |
D-EE (RRID:SCR_019058) | software application, data processing software, data visualization software, data analysis software, software resource | Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup. | Distributed dimensionality reduction, dimensionality reduction, distributed storage, distributed computation, large scale data, single cell data, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:d-ee | https://bio.tools/d-ee | SCR_019058 | 2026-02-16 09:49:35 | 1 | ||||||||
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Neutron Scattering Length and Cross Sections Resource Report Resource Website 1+ mentions |
Neutron Scattering Length and Cross Sections (RRID:SCR_019140) | service resource, data or information resource | Web tool for thermal neutron cross sections. Data of scattering lengths and corresponding scattering and absorption cross sections of elements. Data go through element number 96Cm. Used for study of condensed matter structure and dynamics. | NIST Center for Neutron Research, thermal neutron cross sections, scattering lengths, condensed matter, condensed matter structure, condensed matter dynamics, absorption cross sections, scattering cross sections, data | DOI:10.1080/10448639208218770 | Free, Freely available | SCR_019140 | 2026-02-16 09:49:37 | 4 | ||||||||||
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SoftWoRx software Resource Report Resource Website 10+ mentions |
SoftWoRx software (RRID:SCR_019157) | software application, data processing software, data visualization software, image processing software, image acquisition software, image analysis software, software resource, data acquisition software | Software for acquisition, deconvolution, processing, analysis, and display of DeltaVision images. Used in DeltaVision OMX SR imaging system., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | GE Healthcare, DeltaVision OMX SR, imaging system, image, data | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_019157 | softWoRx 7.0, softWoRx 6.5.2 | 2026-02-16 09:49:37 | 34 | ||||||||||
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SoupX Resource Report Resource Website 50+ mentions |
SoupX (RRID:SCR_019193) | software application, data processing software, software toolkit, data analysis software, software resource | Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. | Estimation, removal, cell free mRNA contamination, droplet based, single cell RNA-seq data, RNA-seq data, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:soupx | https://bio.tools/soupx | SCR_019193 | 2026-02-16 09:49:42 | 77 |
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