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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | software application, data analysis software, software resource, data processing software, data visualization software, 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 | 2026-07-28 09:44:25 | 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 | software application, data analysis software, software resource, data processing software, 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 | 2026-07-28 09:44:23 | 5 | |||||||||
|
VectorMap Resource Report Resource Website 10+ mentions |
VectorMap (RRID:SCR_016721) | service resource, data or information resource, data repository, database, data access protocol, software resource, web service, storage service resource, portal | 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 | 2026-07-28 09:44:25 | 22 | ||||||||
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SMI BeGaze Resource Report Resource Website 1+ mentions |
SMI BeGaze (RRID:SCR_016648) | SMI BeGaze | software application, data analysis software, software resource, data processing software, data visualization software, standalone software, software toolkit | 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 | 2026-07-28 09:44:24 | 7 | |||||||||
|
circular statistics Resource Report Resource Website 10+ mentions |
circular statistics (RRID:SCR_016651) | CircStat | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:44:20 | 42 | |||||
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XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | software application, data analysis software, sequence analysis software, software resource, data processing 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 | 2026-07-28 09:44:22 | 1 | ||||||||
|
LoomPy Resource Report Resource Website 10+ mentions |
LoomPy (RRID:SCR_016666) | LoomPy | software application, software library, software resource, data processing software, data storage software, software toolkit | 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 | 2026-07-28 09:44:24 | 34 | |||||||
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Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | software application, data analysis software, sequence analysis software, software resource, data processing 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 | 2026-07-28 09:44:20 | 9 | ||||||
|
PaVE Resource Report Resource Website 100+ mentions |
PaVE (RRID:SCR_016599) | PaVE | service resource, web application, data or information resource, data analysis service, database, software resource, production service resource, analysis service resource | 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 | 2026-07-28 09:44:18 | 125 | ||||||
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TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | service resource, disease-related portal, data or information resource, organization portal, data repository, topical portal, consortium, storage service resource, 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 | 2026-07-28 09:44:22 | 12 | |||||
|
Open Reading Frame Finder Resource Report Resource Website 1000+ mentions |
Open Reading Frame Finder (RRID:SCR_016643) | ORF finder | software application, service resource, data analysis software, sequence analysis software, data processing software, software resource, production service resource, analysis service resource | Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long. | search, open, reading, frame, DNA, sequence, ORF, protein, translation, data, encoding, segment, verify |
uses: BLASTP has parent organization: NCBI |
Free, Available for download, Freely available | SCR_016643 | Open Reading Frame finder, Open Reading Frame Finder | 2026-07-28 09:44:20 | 1428 | ||||||||
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Walter Reed Biosystematics Unit Resource Report Resource Website 1+ mentions |
Walter Reed Biosystematics Unit (RRID:SCR_016729) | WRBU | data or information resource, organism-related portal, topical portal, portal | National resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections. | medically, important, arthropods, maintanace, repository, U.S. mosquito, data, vector, collection | is parent organization of: VectorMap | SCR_016729 | The Walter Reed Biosystematics Unit, WRBU, Walter Reed Biosystematics Unit | 2026-07-28 09:44:26 | 5 | |||||||||
|
RnaSeqGeneEdgeRQL Resource Report Resource Website |
RnaSeqGeneEdgeRQL (RRID:SCR_016699) | software application, data analysis software, software resource, data processing software, software toolkit | Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment. | study, analysis, RNA, sequencing, read, alignment, data | is affiliated with: Bioconductor | Free, Available for download, Freely available | SCR_016699 | 2026-07-28 09:44:25 | 0 | ||||||||||
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HASP Resource Report Resource Website |
HASP (RRID:SCR_016615) | HASP | software application, data or information resource, database, software resource, data processing software, data visualization software | Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. | structural, visualization, phylogenetic, biochemical, immunological, hemagglutinin, data, 3D, |
is listed by: NIAID is listed by: NIDDK Information Network (dkNET) |
NIAID | DOI:10.1186/1471-2105-14-197 | Free, Freely available | SCR_016615 | HemAgglutinin Structure Prediction, Hemagglutinin Structure Prediction | 2026-07-28 09:44:19 | 0 | ||||||
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Cleveland Children's Sleep and Health Study Resource Report Resource Website |
Cleveland Children's Sleep and Health Study (RRID:SCR_016584) | CCSHS | disease-related portal, data or information resource, topical portal, portal | Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR. | data, pediatric, cohort, sleep, study, EEG, ECG, EOG, EMG, SpO2, polysomnography | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | PMID:12712055 PMID:16335483 DOI:10.1080/15402002.2013.825838 |
SCR_016584 | Cleveland Children's Sleep and Health Study | 2026-07-28 09:44:21 | 0 | |||||||
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Best Apnea Interventions for Research (BestAIR) sleep study Resource Report Resource Website 1+ mentions |
Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) | BestAIR | disease-related portal, data or information resource, topical portal, portal | Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume. | data, analysis, sleep, apnea, treatment, cardiovascular, disease, risk, factor, polysomnography, ECG, SpO2 | is listed by: National Sleep Research Resource (NSRR) | sleep apnea, cardiovascular disease | ResMed Foundation ; Philips Respironics ; NHLBI U34 HL105277 |
DOI:10.5665/sleep.4266 | SCR_016583 | bestair, , Best Apnea Interventions for Research, Bestair | 2026-07-28 09:44:21 | 2 | ||||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | software application, data analysis software, software resource, data processing software, data visualization software | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-07-28 09:44:26 | 21 | ||||||||
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rCASC Resource Report Resource Website 1+ mentions |
rCASC (RRID:SCR_017005) | software application, software resource, data analysis software, data processing software | Software package for reproducible classification analysis of single cell sequencing data. | reproducibility, classification, analysis, single, cell, sequencing, data, bio.tools |
is used by: Stardust is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
PMID:24204232 | Free, Available for download, Freely available | biotools:rCASC | https://kendomaniac.github.io/rCASC/, https://bio.tools/rCASC | SCR_017005 | rCASC, reproducible Cluster Analysis of Single Cells | 2026-07-28 09:44:30 | 1 | ||||||
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INCF-Neurobot Resource Report Resource Website 10+ mentions |
INCF-Neurobot (RRID:SCR_017004) | INCF Neurobot | software application, software resource, data management software, data processing software | Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis. | data, management, clinical, study, brain, traumatic, injury |
has parent organization: Karolinska Institute; Stockholm; Sweden has parent organization: International Neuroinformatics Coordinating Facility |
Registration required | SCR_017004 | , International Neuroinformatics Coordinating Facility Neurobot, INCF Neurobot | 2026-07-28 09:44:26 | 16 | ||||||||
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Stemformatics Resource Report Resource Website 1+ mentions |
Stemformatics (RRID:SCR_017002) | service resource, data set, data or information resource, organization portal, portal | Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. | gene, expression, data, stem, cell, community, microarray, RNA, sequencing, dataset, cluster | ARC Special Research Initiative to Stem Cells Australia ; ARC Discovery Project ; ARC Future Fellowship ; JEM Research Foundation philanthropic funding ; QLD Government Smart Futures Fellowship ; University of Melbourne Centre for Stem Cell Systems |
PMID:23466562 | Free, Available for download, Freely available | SCR_017002 | 2026-07-28 09:44:27 | 1 |
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