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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TRIAGE Resource Report Resource Website 1+ mentions |
TRIAGE (RRID:SCR_016609) | TRIAGE | production service resource, data analysis service, web application, software resource, service resource, analysis service 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 | 2026-08-14 09:27:36 | 1 | |||||||
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Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data processing software, software application, data analysis software, data analytics software, software resource, sequence analysis software | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-08-14 09:27:47 | 0 | |||||||
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Walter Reed Biosystematics Unit Resource Report Resource Website 1+ mentions |
Walter Reed Biosystematics Unit (RRID:SCR_016729) | WRBU | organism-related portal, data or information resource, portal, topical 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 | 2026-08-14 09:27:28 | 5 | |||||||||
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Apnea, Bariatric surgery, and CPAP study Resource Report Resource Website 1+ mentions |
Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) | ABC study | data or information resource, portal, disease-related portal, topical portal | Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore. | dataset, bariatric, surgery, continuous, positive, airway, pressure, therapy, sleep, apnea, obesity II | is listed by: National Sleep Research Resource (NSRR) | class II obesity, obstructive sleep apnea | NHLBI R01 HL106410; NHLBI K24 HL127307 |
DOI:10.1164/rccm.201708-1637LE | Free, Available for public download, Registration required | SCR_016575 | and Cpap study, Bariatric surgery, Apnea | 2026-08-14 09:27:26 | 1 | |||||
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MutaGene Resource Report Resource Website 10+ mentions |
MutaGene (RRID:SCR_016574) | data processing software, software application, data analysis software, software resource | Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity. | analyze, mutagenic, factor, turmor, decipher, cancer, genetic, heterogeneity | is listed by: OMICtools | National Library of Medicine ; NIH |
PMID:28472504 | Free, Available for download, Freely available | https://ncbiinsights.ncbi.nlm.nih.gov/tag/mutagene/ | SCR_016574 | 2026-08-14 09:27:36 | 10 | |||||||
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Appion Package Resource Report Resource Website 10+ mentions |
Appion Package (RRID:SCR_016734) | Appion | image processing software, image analysis software, data processing software, software application, software resource | 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 | 2026-08-14 09:27:38 | 16 | |||||||
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RnaSeqGeneEdgeRQL Resource Report Resource Website |
RnaSeqGeneEdgeRQL (RRID:SCR_016699) | software toolkit, data processing software, software application, data analysis software, software resource | 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 | 2026-08-14 09:27:28 | 0 | ||||||||||
|
CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | data processing software, software application, data analysis software, software resource | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-08-14 09:27:28 | 114 | ||||||||
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SABRe CVD Initiative Resource Report Resource Website |
SABRe CVD Initiative (RRID:SCR_016572) | SABRe CVD | data or information resource, portal, disease-related portal, topical portal | Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation. | generate, biomarker, discovery, data, Framingham, Heart, Study, gene, expression, omicdata | cardiovascular disease, atherosclerosis | Free, Partially available for public, Requested authorized access | SCR_016572 | Systems Approach to Biomarker Research in CardioVascular Disease | 2026-08-14 09:27:26 | 0 | ||||||||
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SpectraVis Resource Report Resource Website |
SpectraVis (RRID:SCR_016691) | data processing software, web application, software application, data analysis software, network analysis software, network graph visualization software, software resource, data visualization software | Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity. | functional, brain, conectivity, analyzing, network, time, frequency | Free, Available for download, Freely available | http://ericdeno.com/research/SpectraVis/ | SCR_016691 | 2026-08-14 09:27:49 | 0 | ||||||||||
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HASP Resource Report Resource Website |
HASP (RRID:SCR_016615) | HASP | database, data processing software, data or information resource, software application, software resource, 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 | 2026-08-14 09:27:36 | 0 | ||||||
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KAT Resource Report Resource Website 10+ mentions |
KAT (RRID:SCR_016741) | KAT | software toolkit, data processing software, software application, data analysis software, software resource | Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies. | generate, analyse, compare, k-mer, spectra, sequence, file, quality, control, NGS, dataset, genome, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC | DOI:10.1093/bioinformatics/btw663 | Free, Available for download, Freely available | biotools:kat | http://www.earlham.ac.uk/kat-tools, https://bio.tools/kat | SCR_016741 | K-mer Analysis Toolkit | 2026-08-14 09:27:38 | 21 | ||||
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Cleveland Children's Sleep and Health Study Resource Report Resource Website 1+ mentions |
Cleveland Children's Sleep and Health Study (RRID:SCR_016584) | CCSHS | data or information resource, portal, disease-related portal, topical 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 | 2026-08-14 09:27:46 | 1 | |||||||
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Imaging WorkBench Resource Report Resource Website 1+ mentions |
Imaging WorkBench (RRID:SCR_016589) | IW | image analysis software, data processing software, software application, software resource, image acquisition software, data acquisition software | Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems. | multichannel, fluorescence, image, acquisition, analysis | Commercially available | SCR_016589 | IW 6, Imaging Workbench 6.0, Imaging Workbench (IW) 6, IW 6.0, Imaging Workbench 6 | 2026-08-14 09:27:36 | 5 | |||||||||
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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 | data or information resource, portal, disease-related portal, topical 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 | 2026-08-14 09:27:26 | 3 | ||||||
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kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | data processing software, software application, data analysis software, software resource | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html, https://bio.tools/kallisto, https://sources.debian.org/src/kallisto/ | SCR_016582 | kallisto v0.43.1 | 2026-08-14 09:27:36 | 148 | ||||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | data processing software, software application, data analysis software, software resource, 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 | 2026-08-14 09:27:53 | 23 | ||||||||
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rCASC Resource Report Resource Website 1+ mentions |
rCASC (RRID:SCR_017005) | data processing software, software application, data analysis software, software resource | 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 | 2026-08-14 09:27:55 | 1 | ||||||
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INCF-Neurobot Resource Report Resource Website 10+ mentions |
INCF-Neurobot (RRID:SCR_017004) | INCF Neurobot | data processing software, software application, software resource, data management 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 | 2026-08-14 09:27:31 | 17 | ||||||||
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Stemformatics Resource Report Resource Website 1+ mentions |
Stemformatics (RRID:SCR_017002) | portal, data or information resource, data set, service resource, organization 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 | 2026-08-14 09:27:55 | 1 |
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