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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mia Resource Report Resource Website 10+ mentions |
mia (RRID:SCR_023619) | data analysis software, data processing software, software resource, software application | Software R package with several tools for microbiome data analysis. | microbiome data, microbiome data analysis, | is related to: R Project for Statistical Computing | Free, Available for download, Freely available | https://github.com/microbiome/mia | SCR_023619 | 2026-08-13 09:30:48 | 10 | |||||||||
|
Alfred Resource Report Resource Website 10+ mentions |
Alfred (RRID:SCR_023354) | web application, software resource, algorithm resource | Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas. | alignment, BAM, quality control, cell barcode splitting, annotation directed improvement, BAM alignment statistics, feature counting, feature annotation. | NHGRI U41HG007497 | PMID:30520945 | Free, Available for download, Freely available | https://bio.tools/alfred | SCR_023354 | 2026-08-13 09:31:02 | 18 | ||||||||
|
BlobTools2 Resource Report Resource Website 100+ mentions |
BlobTools2 (RRID:SCR_023351) | data analysis software, data processing software, software resource, software application | Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier. | interactive quality assessment, genome assemblies, identifying and isolating non-target data, genome, QC, filtering, process assembly, read and analysis files, |
is related to: Blobtools is related to: Blobtoolkit |
BBSRC Bioinformatics and Biological Resources fund | PMID:32071071 | Free, Available for download, Freely available | https://github.com/blobtoolkit/blobtoolkit | SCR_023351 | blobtoolkit | 2026-08-13 09:30:44 | 383 | ||||||
|
BigSeqKit Resource Report Resource Website 1+ mentions |
BigSeqKit (RRID:SCR_023592) | software toolkit, software resource, software library | Software parallel Big Data toolkit to process FASTA and FASTQ files at scale. Used to manipulate FASTA/Q files at scale with speed and scalability at its core. | FASTA file, Q file, file manipulation, process FASTA and FASTQ files, | Free, Available for download, Freely available | SCR_023592 | 2026-08-13 09:30:48 | 1 | |||||||||||
|
TIGER Data Portal Resource Report Resource Website 10+ mentions |
TIGER Data Portal (RRID:SCR_023626) | topical portal, data or information resource, disease-related portal, portal | Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets. | Type 2 Diabetes, genetic and epigenetic, functional data, molecular data, clinical data, pancreatic beta cells. | is related to: T2DSystems | Type 2 Diabetes | European Union Horizon 2020 ; Spanish government ; Swiss State Secretariat for Education‚ Research and Innovation ; American Diabetes Association Innovative and Clinical Translational Award ; Research England ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545 |
PMID:34644572 | SCR_023626 | Translational Human Pancreatic Islet Genotype Tissue-Expression Resource | 2026-08-13 09:31:07 | 23 | |||||||
|
X2K Web Resource Report Resource Website 10+ mentions |
X2K Web (RRID:SCR_023624) | X2K | data access protocol, software resource, web service | Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks. | predicts involvement of upstream cell signaling pathways, differentially expressed genes, linking expression signatures, upstream cell signaling networks, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NHLBI U54 HL127624; NCI U24 CA224260; NIH Office of the Director OT3 OD025467 |
PMID:29800326 | Free, Freely available | https://github.com/MaayanLab/x2k_web | SCR_023624 | eXpression2Kinases (X2K) Web | 2026-08-13 09:31:07 | 25 | |||||
|
UpSetPlot Resource Report Resource Website 1+ mentions |
UpSetPlot (RRID:SCR_023225) | data processing software, software resource, data visualization software, software application | Software Python implementation of UpSet plots to visualize set overlaps. | UpSet plots, Python, visualize set overlaps, | Austrian Science Fund ; Air Force Research Laboratory ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_023225 | 2026-08-13 09:30:43 | 7 | |||||||||
|
Diabetes Data and Hypothesis Hub Resource Report Resource Website 1+ mentions |
Diabetes Data and Hypothesis Hub (RRID:SCR_023629) | D2H2 | topical portal, data or information resource, disease-related portal, database, portal | Platform that facilitates data driven hypothesis generation for diabetes and related metabolic disorder research community. Curated transcriptomics datasets from various Type 2 Diabetes studies are made available for download, visualization, and enrichment analysis. | diabetes, metabolic disorder, diabetes related metabolic disorder, transcriptomics datasets, |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Type 2 Diabetes | Free, Freely available | SCR_023629 | Diabetes Data and Hypothesis Hub (D2H2) | 2026-08-13 09:30:48 | 2 | |||||||
|
Korea Statistical Information Service Resource Report Resource Website 50+ mentions |
Korea Statistical Information Service (RRID:SCR_023565) | data or information resource, data access protocol, software resource, web service | Republic of Korea e-Government platform for major domestic, international and North Korean statistics. Web service provides official statistics produced by statistical agencies covering more than 500 subject matters as well as the latest data on international finance and economy from international organizations i.e. IMF, World Bank, OECD. | Korean statistics, public data, international finance and economy, | Free, Freely available | SCR_023565 | KOSIS | 2026-08-13 09:31:06 | 72 | ||||||||||
|
Children's Hospital Association Pediatric Health Information System Resource Report Resource Website 1+ mentions |
Children's Hospital Association Pediatric Health Information System (RRID:SCR_023168) | PHIS | topical portal, data or information resource, database, portal | Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals. | Children's hospitals, PHIS database, pediatrics data, clinical and resource utilization data, inpatient data, ambulatory surgery data, emergency department data, observation unit data | Free, Freely available | SCR_023168 | Pediatric Health Information System | 2026-08-13 09:30:59 | 5 | |||||||||
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BLIMP: Biomedical LIterature Mining Publications Resource Report Resource Website 1+ mentions |
BLIMP: Biomedical LIterature Mining Publications (RRID:SCR_007112) | BLIMP | data or information resource, bibliography | Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication. | biomedical, literature, text mining, bibliography, journal, text, biomedicine, natural language processing, information extraction, information retrieval, text categorization, ontology | has parent organization: Queens University; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada ; Queen's University Principal's Development Award ; NSERC Discovery 298292-04 |
The community can contribute to this resource | nif-0000-21063 | SCR_007112 | Biomedical LIterature (and text) Mining Publications | 2026-08-13 09:27:44 | 1 | ||||||
|
MetaFluor Fluorescence Ratio Imaging Software Resource Report Resource Website 1+ mentions |
MetaFluor Fluorescence Ratio Imaging Software (RRID:SCR_014331) | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software designed to take single or multi-wavelength intracellular ion measurements an provide simultaneous display of the raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image for microscope techniques such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities. | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014331 | 2026-08-13 09:29:10 | 2 | ||||||||||||
|
ObjectFinder Resource Report Resource Website 1+ mentions |
ObjectFinder (RRID:SCR_023319) | data or information resource, data processing software, software application, image analysis software, image, 3d visualization software, data visualization software, 3d spatial image, 2d spatial image, software resource | Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes. | 3D object recognition, volumetric images, neuroscience, recognize small structures in large volumetric images, detect fluorescently labeled synapses, neuronal image stacks, | is related to: MATLAB | https://lucadellasantina.github.io/ObjectFinder/ | SCR_023319 | 2026-08-13 09:31:01 | 7 | ||||||||||
|
xyz2swc Resource Report Resource Website 1+ mentions |
xyz2swc (RRID:SCR_023317) | data access protocol, software resource, web service | Web service that converts all 30 reconstruction formats (and 65 variations) described in scientific literature into SWC standard. Service is available open-source through user-friendly browser interface and Application Programming Interface. | reconstruction formats conversion, formats conversion into SWC standard, SWC standard, | is related to: NeuroMorpho.Org | Free, Freely available | https://neuromorpho.org/xyz2swc/ | SCR_023317 | 2026-08-13 09:31:03 | 3 | |||||||||
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Variant Prediction Tools Evaluation Resource Report Resource Website 1+ mentions |
Variant Prediction Tools Evaluation (RRID:SCR_023314) | VETA | data analysis software, data processing software, software resource, software application | Software tool that analyses performance of several variant prediction methods at different levels. Used to benchmark variant effect predictors from VCF files. | variant prediction, benchmark variant effect predictors, VCF files | is related to: Benchmark of human deep intronic variation | DOI:10.3389/fcvm.2022.975478 | Free, Available for download, Freely available | https://samtools.github.io/hts-specs/VCFv4.2.pdf | SCR_023314 | Variant prEdiction Tools evAluation | 2026-08-13 09:30:44 | 2 | ||||||
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Michigan Genomics Initiative Resource Report Resource Website 1+ mentions |
Michigan Genomics Initiative (RRID:SCR_023556) | MGI | data or information resource, project portal, service resource, storage service resource, material storage repository, biobank, portal | Collaborative research effort among physicians, researchers, and patients at the University of Michigan with goal of combining patient electronic health record data with corresponding genetic data to gain novel biomedical insights. Biobank linking genotypes and electronic clinical records in Michigan Medicine patients. MGI participants agree to provide study team with access to EHR data for clinical information and biospecimen including blood or saliva. | combining patient electronic health record data, genetic data, genotypes, electronic clinical records | has parent organization: Michigan State University; Michigan; USA | PMID:36819667 | Restricted | SCR_023556 | 2026-08-13 09:31:06 | 6 | ||||||||
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DendroX Resource Report Resource Website 1+ mentions |
DendroX (RRID:SCR_023434) | data processing software, software application, data visualization software, 4d visualization software, source code, software resource | Web application for multi-level multi-cluster selections in dendrogram. Provides interactive visualization of dendrogram in which users can divide dendrogram at any level and into any number of clusters. | cluster, heatmap, visualization, dendrogram, cluster analysis, TypeScript | Second Military Medical University 2017JZ11; Shanghai Jiading District Health Commission 2020-ZD-01 |
Free, Available for download, Freely available | https://frlender.github.io/dendrox-app/ | SCR_023434 | 2026-08-13 09:30:46 | 1 | |||||||||
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UCSC Cell Browser Resource Report Resource Website 100+ mentions |
UCSC Cell Browser (RRID:SCR_023293) | data access protocol, software resource, web service | Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes. | visualize gene expression, metadata annotation distribution, single cell data viewer, cluster specific marker genes, single cell expression, |
is related to: Allen Institute for Brain Science is related to: BRAIN Initiative Cell Atlas Network has parent organization: University of California at Santa Cruz; California; USA |
NHGRI 5U41HG002371; NHGRI 1U41HG010972; NHGRI 5R01HG010329; NIMH U01MH114825; NINDS K99 NS111731; NIMH RF1MH121268; NIMH DP2MH122400; Silicon Valley Community Foundation ; California Institute for Regenerative Medicine ; University of California Office of the President Emergency COVID-19 Research Seed Funding ; Chan Zuckerberg Initiative Foundation ; Simons Foundation ; Brain and Behavior Research Foundation |
PMID:34244710 | Free, Freely available | https://cellbrowser.readthedocs.io/en/master/, https://github.com/maximilianh/cellBrowser | SCR_023293 | 2026-08-13 09:30:44 | 155 | |||||||
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Musculoskeletal Knowledge Portal Resource Report Resource Website 10+ mentions |
Musculoskeletal Knowledge Portal (RRID:SCR_023171) | MSK-KP | topical portal, data or information resource, disease-related portal, portal | Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data. | genomic data mining, human genetic data, genomic information, musculoskeletal traits and diseases data, DRKB | musculoskeletal disease | NIH AR085003 | PMID:34686856 | Free, Freely available | https://msk.hugeamp.org/ | SCR_023171 | 2026-08-13 09:31:01 | 26 | ||||||
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roifile Resource Report Resource Website 1+ mentions |
roifile (RRID:SCR_023331) | software toolkit, software resource, software library | Software Python package to read, write, create, and plot ImageJ ROI format, an undocumented and ImageJ application specific format to store regions of interest, geometric shapes, paths, text, and whatnot for image overlays. | Python package, plot ImageJ ROIs, store regions of interest, geometric shapes, paths, text, image overlays | Free, Available for download, Freely available | SCR_023331 | 2026-08-13 09:30:44 | 1 |
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