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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | analysis service resource, data analysis service, data management software, production service resource, service resource, software application, software resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-09-12 12:58:39 | 2 | |||||||
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FCS Express Resource Report Resource Website 500+ mentions |
FCS Express (RRID:SCR_016431) | data analysis software, data processing software, software application, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2026-09-12 12:58:39 | 518 | ||||||||||
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Sleep Heart Health Study Resource Report Resource Website 50+ mentions |
Sleep Heart Health Study (RRID:SCR_016559) | SHHS | data or information resource, disease-related portal, portal, topical portal | Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light. | dataset, analysis, sleep, apnea, breathing, disorder, cardiovascular, disease, EEG, ECG, respiration, PSG | is listed by: National Sleep Research Resource (NSRR) | sleep disorder, sleep apnea, cardiovascular disease | NHLBI U01 HL53916; NHLBI U01 HL53931; NHLBI U01 HL53934; NHLBI U01 HL53937; NHLBI U01 HL53938; NHLBI U01 HL53941; NHLBI U01 HL64360 |
PMID:9493915 | Free, Freely available, Registration required for membership | SCR_016559 | Sleep Heart Health Study | 2026-09-12 12:58:41 | 84 | |||||
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SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | data analysis software, data analytics software, data processing software, software application, software resource | Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis. | single, cell, RNA seq, data, sorted, whole, organ, profiling, analysis | NHLBI R01 HL105433; NHLBI U01 HL110964; NHLBI U01 HL122642 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-09-12 12:58:41 | 5 | ||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data analysis software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | MIB, Microscopy Image Browser | 2026-09-12 12:58:41 | 160 | ||||
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VPV Resource Report Resource Website 1+ mentions |
VPV (RRID:SCR_016545) | VPV | 3d visualization software, data processing software, data visualization software, software application, software resource | Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph. | Phyton, desktop, 3D viewer, analysis, results, phenotype, detection, LAMA pipeline | is listed by: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | SCR_016545 | Volume Phenotype Viewer, volume phenotype viewer | 2026-09-12 12:58:41 | 1 | ||||||||
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RNA22 Resource Report Resource Website 100+ mentions |
RNA22 (RRID:SCR_016507) | RNA22 | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases. | pattern, based, detecting, microRNA, binding, site, complex, sequence, genome, analysis, FASEB list | is listed by: OMICtools | A Star ; Singapore ; NIDDK DK04763; NIH AI54973 |
Free, Available for download, Freely available | SCR_016507 | RiboNucleic Acid 22 | 2026-09-12 12:58:40 | 222 | |||||||
|
Thermo Fisher: GeneChip� Scanner 3000 7G Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk, https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-09-12 12:58:40 | 1 | |||||||||
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UAMH Centre for Global Microfungal Biodiversity Resource Report Resource Website 1+ mentions |
UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) | biomaterial supply resource, material resource, organism supplier | Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi. | microbial, repository, collection, preservation, analysis, identification, fungi | is related to: University of Toronto; Ontario; Canada | SCR_016466 | 2026-09-12 12:58:40 | 5 | |||||||||||
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Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | data or information resource, database, organism-related portal, portal, topical portal | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the National Science Foundation for Young Scientists of China ; the Strategic Priority Research Program of the Chinese Academy of Sciences |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-09-12 12:58:40 | 5 | |||||
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iMaps Resource Report Resource Website 10+ mentions |
iMaps (RRID:SCR_016705) | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource | Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions. | Genialis, analysis, high-resolution, sequencing, data, RNA, DNA, protein, interaction |
is related to: iCount is related to: iCount |
Free, Registration required | SCR_016705 | 2026-09-12 12:58:43 | 11 | ||||||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | 2026-09-12 12:58:43 | 33 | ||||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data analysis software, data processing software, software application, software resource | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html, https://hub.docker.com/r/tomazc/icount/ | SCR_016712 | 2026-09-12 12:58:43 | 39 | |||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | data analysis software, data processing software, data visualization software, image analysis software, software application, software resource | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html, | SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-09-12 12:58:43 | 5 | ||||||
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BD FACS Sortware sorter software Resource Report Resource Website 1+ mentions |
BD FACS Sortware sorter software (RRID:SCR_016722) | BD FACS Sortware software | data analysis software, data processing software, data visualization software, software application, software resource | Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems. | control, cell, sorter, acquisition, analysis, integrate, data, instrument, system, Becton Dickinson and Company | Commercially available | SCR_016722 | , BD FACS Sortware, Becton Dickinson FACS Sortware, BD FACS Sortware software | 2026-09-12 12:58:43 | 5 | |||||||||
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fermi Resource Report Resource Website |
fermi (RRID:SCR_016652) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes. | assembler, analysis, whole, genome, short, gun, sequencing, error, correction | is listed by: OMICtools | NHGRI U01 HG005208 | PMID:22569178 | Free, Available for download, Freely available | SCR_016652 | 2026-09-12 12:58:42 | 0 | ||||||||
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MetaXpress Resource Report Resource Website 500+ mentions |
MetaXpress (RRID:SCR_016654) | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging. | Molecular Devices, ImageXpress, high, content, image, analysis, acquisition, time, lapse, 2D, 3D, cellular, imaging | Commercially available | SCR_016654 | 2026-09-12 12:58:42 | 657 | |||||||||||
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Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
NHGRI R01 HG006677; NIGMS R01 GM083873; NSF ABI1356078; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | 2026-09-12 12:58:43 | 10 | ||||||
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PaVE Resource Report Resource Website 100+ mentions |
PaVE (RRID:SCR_016599) | PaVE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, web application | Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information. | data, curated, papilloma, virus, genomic, sequence, analysis, storage, annotation, FASEB list | is listed by: NIAID | NIAID ZIA AI001071 | PMID:28053164 | Open source | SCR_016599 | PapillomaVirus Episteme, Papillomavirus Episteme | 2026-09-12 12:58:42 | 156 | ||||||
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TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | consortium, data or information resource, data repository, disease-related portal, organization portal, portal, service resource, storage service resource, topical portal | Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data. | collect, data, sharing, analysis, tuberculosis, global, bio.tools |
is listed by: NIAID is listed by: bio.tools is listed by: Debian |
tuberculosis | NIH | DOI:10.1128/JCM.01013-17 | Free, Freely available | r3d100013925, biotools:TB_Portals | https://bio.tools/TB_Portals, https://doi.org/10.17616/R31NJN8L | SCR_016594 | 2026-09-12 12:58:42 | 20 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
