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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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iMaps Resource Report Resource Website 10+ mentions |
iMaps (RRID:SCR_016705) | production service resource, data analysis service, portal, data or information resource, service resource, analysis 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 | 2026-08-14 09:27:28 | 11 | ||||||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | production service resource, data analysis service, web application, software resource, service resource, analysis service 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 | 2026-08-14 09:27:49 | 33 | ||||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data processing software, software application, data analysis software, 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 | 2026-08-14 09:27:28 | 39 | |||||||||
|
INC-Seq Resource Report Resource Website |
INC-Seq (RRID:SCR_016711) | INC-Seq | data processing software, software application, data analysis software, software resource, sequence analysis software | Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities. | accurate, single, molecule, read, nanopore, sequencing, 16S rRNA, bacteria | is related to: NanoAmpli-Seq | Agency for Science ; Technology and Research ; Singapore |
PMID:27485345 | Free, Available for download, Freely available | https://zenodo.org/record/57405#.W-nb0pNKiM8 | SCR_016711 | Intramolecular ligated Nanopore Consensus Sequencing, INC-Seq | 2026-08-14 09:27:37 | 0 | |||||
|
NanoAmpli-Seq Resource Report Resource Website 1+ mentions |
NanoAmpli-Seq (RRID:SCR_016710) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing. | amplicon, sequencing, 16S rRNA, mixed, microbial, communities, nanopore, platform, gene |
is related to: INC-Seq has parent organization: University of Glasgow; Glasgow; United Kingdom |
EPSRC EP/M016811/1; NERC NE/L011956/1 |
DOI:10.1101/244517 | Free, Available for download, Freely available | https://www.protocols.io/view/nanoampli-seq-bioinformatics-workflow-u25eyg6 | SCR_016710 | 2026-08-14 09:27:49 | 1 | |||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | image analysis software, data processing software, software application, data analysis software, software resource, data visualization 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 | 2026-08-14 09:27:28 | 5 | ||||||
|
Florida State University Physical Biochemistry Core Facility Resource Report Resource Website 1+ mentions |
Florida State University Physical Biochemistry Core Facility (RRID:SCR_016714) | PBF | core facility, production service resource, access service resource, availability annotation standard, standard specification, the community can contribute to this resource, training service resource, data or information resource, nif annotation standard, material service resource, service resource, narrative resource | Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students. | core, facility, biophysical, study, macromolecule, providing, resource, instrument, training, guidance, student, Florida, State, University |
has parent organization: Florida State University; Florida; USA has parent organization: Institute of Molecular Biophysics at Florida State University; Florida; USA |
Restricted | SCR_016714 | The Physical Biochemistry Facility (PBF), The Physical Biochemistry Facility, Physical Biochemistry Facility | 2026-08-14 09:27:49 | 1 | ||||||||
|
Stitching Resource Report Resource Website 1+ mentions |
Stitching (RRID:SCR_016568) | image analysis software, image processing software, data processing software, software application, software resource, image reconstruction software | Software package available through Fiji to image large biological specimen at high resolution. Comes with 2 different plugins to reconstruct big images/stacks : Pairwise Stitching to stitch two 2d-5d images, and Grid/Collection Stitching to stitch an arbitrary amount of 2d-5d input images. | biological, speciment, resoultion, reconstruct, big, image, stack, stitching | Free, Available for download, Freely available | https://github.com/fiji/Stitching/releases/tag/Stitching_-3.1.3 | SCR_016568 | 2026-08-14 09:27:36 | 4 | ||||||||||
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University of FLorida College of Medicine Molecular Pathology Core Facility Resource Report Resource Website 10+ mentions |
University of FLorida College of Medicine Molecular Pathology Core Facility (RRID:SCR_016601) | MPC | service resource, access service resource, core facility | Histology and light microscopy facility for paraffin and frozen blocks and all aspects of sample preparation, fixation, embedding, sectioning, staining, and imaging. Consultations, technical assistance and training are also provided. Standard operating procedures compliant with good laboratory and clinical processes are followed for all procedures. Services include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays.. | histology, immunohistochemistry, sample processing, clinical research, cryosectioning, imaging, staining, immunfluorescence, microarrays, core facility |
has parent organization: University of Florida Labs and Facilities has parent organization: University of Florida; Florida; USA |
Restricted | SCR_001055, SciEx_8810 | http://www.scienceexchange.com/facilities/molecular-pathology-core-ufl | SCR_016601 | Molecular Pathology Core, , University of Florida Molecular Pathology Core | 2026-08-14 09:27:27 | 17 | ||||||
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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 processing software, software application, data analysis software, software resource, data visualization software | 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 | 2026-08-14 09:27:50 | 5 | |||||||||
|
VectorMap Resource Report Resource Website 10+ mentions |
VectorMap (RRID:SCR_016721) | database, data repository, storage service resource, portal, web service, data or information resource, data access protocol, software resource, service resource | Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap. | disease, map, collection, data, distribution, model, arthropod, disease, vector, species | has parent organization: Walter Reed Biosystematics Unit | arthropod disease | US Department of Defense Global Emerging Infections Surveillance and Response System ; Division of the Armed Forces Health Surveillance Center ; Global Biodiversity Information System |
Public, Free, Available for download, Freely available, Acknowledgement requested, Tutorial available | SCR_016721 | 2026-08-14 09:27:28 | 28 | ||||||||
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SMI BeGaze Resource Report Resource Website 1+ mentions |
SMI BeGaze (RRID:SCR_016648) | SMI BeGaze | software toolkit, standalone software, data processing software, software application, data analysis software, software resource, data visualization software | Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results. | eye, tracking, study, New Bio Technology Ltd, recording, analyzing, visualizing, data | Commercially available | SCR_016648 | SMI BeGaze™, SMI BehavioralGaze, SMI Behavioral and Gaze Analysis | 2026-08-14 09:27:48 | 7 | |||||||||
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metaPocket Resource Report Resource Website 10+ mentions |
metaPocket (RRID:SCR_016653) | simulation software, production service resource, software application, software resource, service resource, analysis service resource | Software tool to identify pockets on protein surface to predict ligand-binding sites. | protein, surface, prediction, ligand, binding, site, identify, pocket | is listed by: OMICtools | Ministry of Science and Technology (MOST) China ; EU 7th Framework Marie Curie Actions of International Research Staff Exchange Scheme (IRSES) |
PMID:19645590 PMID:21636590 |
Free for academic users, Freely available | http://sysbio.zju.edu.cn/metapocket | SCR_016653 | metaPocket, metaPocket 2.0 | 2026-08-14 09:27:37 | 41 | ||||||
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fermi Resource Report Resource Website |
fermi (RRID:SCR_016652) | data processing software, software application, data analysis software, software resource, sequence analysis software | 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 | 2026-08-14 09:27:48 | 0 | ||||||||
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circular statistics Resource Report Resource Website 10+ mentions |
circular statistics (RRID:SCR_016651) | CircStat | data processing software, software application, data analysis software, software resource | Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data. | circular, inferential, statistics, directional, data |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany works with: MATLAB |
German National Academic Foundation ; German Ministry of Education ; Science ; Research and Technology |
DOI:10.18637/jss.v031.i10 | Free, Available for download, Registration required to MathWorks Account, | https://github.com/circstat/circstat-matlab | SCR_016651 | Matlab Circular Statistics Toolbox, , circstat-matlab, circular statistics, Circular Statistics, CircStat for Matlab | 2026-08-14 09:27:27 | 47 | |||||
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MetaXpress Resource Report Resource Website 500+ mentions |
MetaXpress (RRID:SCR_016654) | image analysis software, data processing software, software application, software resource, image acquisition software, data acquisition 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 | 2026-08-14 09:27:27 | 657 | |||||||||||
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Genotate Resource Report Resource Website |
Genotate (RRID:SCR_016659) | database, web service, data or information resource, data access protocol, software resource | Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts. | identify, explore, visualize, homology, functional, annotation, assemble, transcript, dataset |
works with: Ensembl works with: UniProt works with: NONCODE |
ANR | Free, Available for download, Freely available, | SCR_016659 | 2026-08-14 09:27:37 | 0 | |||||||||
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XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. | correct, technical, bias, sex, chromosome, next, generation, sequencing, data | is listed by: OMICtools | NIGMS R35 GM124827 | DOI:10.1101/346940 | Free, Available for download, Freely available | SCR_016661 | 2026-08-14 09:27:27 | 1 | ||||||||
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LoomPy Resource Report Resource Website 10+ mentions |
LoomPy (RRID:SCR_016666) | LoomPy | software toolkit, data processing software, software application, software resource, data storage software, software library | Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM. | Python, Loom file, format, store, organize, omics, dataset, single, cell, expression, data, HDF5 |
is used by: BICCN works with: loom-viewer works with: Loom |
Free, Available for download, Freely available | https://linnarssonlab.org/loompy/, https://github.com/linnarsson-lab/loompy | SCR_016666 | Loompy v2.0, Loompy v2.0.14, Loom Python, LoomPy, LoomPython | 2026-08-14 09:27:37 | 40 | |||||||
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Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data processing software, software application, data analysis software, software resource, sequence analysis software | 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 | 2026-08-14 09:27:48 | 10 |
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