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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | data processing software, data analysis software, data analytics 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 U01 HL110964; NHLBI U01 HL122642; NHLBI R01 HL105433 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-02-14 02:03:14 | 5 | ||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data visualization software, data processing software, data analysis software, software application, image processing software, 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 | 2026-02-14 02:03:06 | 143 | ||||
|
VPV Resource Report Resource Website 1+ mentions |
VPV (RRID:SCR_016545) | VPV | data visualization software, data processing software, software application, 3d visualization software, 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 | 2026-02-14 02:03:17 | 1 | ||||||||
|
RNA22 Resource Report Resource Website 100+ mentions |
RNA22 (RRID:SCR_016507) | RNA22 | sequence analysis software, data processing software, data 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 | 2026-02-14 02:03:04 | 192 | |||||||
|
GeneChip™ Scanner 3000 7G Resource Report Resource Website 1+ mentions |
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://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-02-14 02:03:05 | 1 | ||||||||||
|
UAMH Centre for Global Microfungal Biodiversity Resource Report Resource Website 1+ mentions |
UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) | biomaterial supply resource, organism supplier, material resource | 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 | 2026-02-14 02:03:13 | 5 | |||||||||||
|
Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | organism-related portal, portal, data or information resource, database, 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 Strategic Priority Research Program 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 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the National Science Foundation for Young Scientists of China |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-02-14 02:03:13 | 5 | |||||
|
iMaps Resource Report Resource Website 1+ mentions |
iMaps (RRID:SCR_016705) | data analysis service, portal, analysis service resource, data or information resource, 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 | 2026-02-14 02:03:08 | 9 | ||||||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | web application, data analysis service, analysis service resource, production service resource, service resource, software resource | 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 | 2026-02-14 02:03:18 | 22 | ||||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:05 | 35 | |||||||||
|
NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | data visualization software, data processing software, data analysis software, software application, software resource, image analysis software | 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 | 2026-02-14 02:03:19 | 5 | ||||||
|
BD FACS Sortware sorter software Resource Report Resource Website 1+ mentions |
BD FACS Sortware sorter software (RRID:SCR_016722) | BD FACS Sortware software | data visualization software, data processing software, data analysis 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 | 2026-02-14 02:03:05 | 5 | |||||||||
|
fermi Resource Report Resource Website |
fermi (RRID:SCR_016652) | sequence analysis software, data processing software, data 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 | 2026-02-14 02:03:07 | 0 | ||||||||
|
MetaXpress Resource Report Resource Website 500+ mentions |
MetaXpress (RRID:SCR_016654) | data processing software, data acquisition software, image acquisition software, software application, software resource, image analysis software | 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 | 2026-02-14 02:03:05 | 621 | |||||||||||
|
Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | sequence analysis software, data processing software, data 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 |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
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 | 2026-02-14 02:03:18 | 9 | ||||||
|
PaVE Resource Report Resource Website 100+ mentions |
PaVE (RRID:SCR_016599) | PaVE | web application, data analysis service, analysis service resource, data or information resource, production service resource, service resource, software resource, database | 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 | 2026-02-14 02:03:07 | 125 | ||||||
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TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | data repository, storage service resource, portal, consortium, data or information resource, organization portal, service resource, disease-related portal, 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 | 2026-02-14 02:03:17 | 12 | |||||
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TRIAGE Resource Report Resource Website 1+ mentions |
TRIAGE (RRID:SCR_016609) | TRIAGE | web application, data analysis service, analysis service resource, production service resource, service resource, software resource | Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies. | prediction, analysis, hypothesis, generation, genome, perturbation, study, RNAi, CRISP | is listed by: NIAID | NIH | Free, Available for download, Freely available | SCR_016609 | Throughput Ranking by Iterative Analysis of Genomic Enrichment | 2026-02-14 02:03:05 | 1 | |||||||
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Appion Package Resource Report Resource Website 10+ mentions |
Appion Package (RRID:SCR_016734) | Appion | data processing software, software application, image processing software, software resource, image analysis software | Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. | processing, analysis, electron, microscope, image | NCRR RR17573; NCRR RR023093; ARCS |
PMID:19263523 | Free, Available for download, Freely available | http://www.appion.org | SCR_016734 | 2026-02-14 02:03:09 | 16 | |||||||
|
dCAS Resource Report Resource Website |
dCAS (RRID:SCR_016612) | dCAS | software resource, web application | Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene | is listed by: NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016612 | Desktop cDNA Annotation System | 2026-02-14 02:03:18 | 0 |
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