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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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StatPlus Mac Resource Report Resource Website 100+ mentions |
StatPlus Mac (RRID:SCR_014635) | data analysis software, data processing software, software application, software resource | A statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program. | statistics, mac, ios, excel, data analysis, software | Available for download | SCR_014635 | StatPlus | 2026-09-12 12:58:20 | 195 | ||||||||||
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BD CellQuest Pro Resource Report Resource Website 1000+ mentions |
BD CellQuest Pro (RRID:SCR_014489) | data acquisition software, data processing software, software application, software resource | A software for acquiring and analyzing flow cytometry data. The user can create plots with elements like regions, gates, statistics, markers, and annotated text. The software can also be used for batch analysis or quality control of analysis. Results can be exported and saved., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis, flow cytometry data acquisition and analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014489 | 2026-09-12 12:58:17 | 3939 | |||||||||||
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Clone Manager Software Resource Report Resource Website 10+ mentions |
Clone Manager Software (RRID:SCR_014521) | data processing software, simulation software, software application, software resource, workflow software | A software system to assist with cloning simulation, enzyme operations, and graphic map drawing. Clone Manager can also be used as a way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. Clone Manager Professional is an upgraded version of Clone Manager Basic., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | workflow software, simulation software, enzyme, clone, cloning simulation, graphic map, sequence, view, edit | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014521 | 2026-09-12 12:58:18 | 49 | |||||||||||
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Core Gene Evaluation Script Resource Report Resource Website 1+ mentions |
Core Gene Evaluation Script (RRID:SCR_014604) | data analysis software, data processing software, software application, software resource | A tool used to screen for core gene sets as an indicator of completeness of draft genomes. The download includes a Perl script and required archaeal and bacterial core genes fasta and cluster files. | microbiome, core gene, draft genome, indicator, microbe, microorganism, software | is listed by: Human Microbiome Project | Available for download | SCR_014604 | 2026-09-12 12:58:19 | 6 | ||||||||||
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inVUE Resource Report Resource Website 1+ mentions |
inVUE (RRID:SCR_014608) | data analysis software, data processing software, data visualization software, software application, software resource | An API and software suite for large scale data visualization and analysis. | microbiome, api, data visualization, data analysis, software | is listed by: Human Microbiome Project | SCR_014608 | 2026-09-12 12:58:19 | 1 | |||||||||||
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RAST Server Resource Report Resource Website 1000+ mentions |
RAST Server (RRID:SCR_014606) | RAST | production service resource, service resource | A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. | microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools |
is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools |
National Science Foundation 0850546; NIAID contract HHSN272200900040C |
PMID:18261238 | Free for the scientific community, Login required | biotools:theseed | https://bio.tools/theseed | SCR_014606 | Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server | 2026-09-12 12:58:19 | 1198 | ||||
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Med Associates Video Freeze Software Resource Report Resource Website 50+ mentions |
Med Associates Video Freeze Software (RRID:SCR_014574) | data acquisition software, data processing software, software application, software resource | Automation software used to analyze fear behavior in rodents. Freezing is represented in the data file in several different ways, including the total time the subject spends motionless during the session, the percent of time motionless, the number of freezing episodes or occurrences, or as an average index of motion. | rodent, freeze, fear, data acquisition, data acquisition software | Commercial | SCR_014574 | 2026-09-12 12:58:18 | 72 | |||||||||||
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Desmond Resource Report Resource Website 500+ mentions |
Desmond (RRID:SCR_014575) | simulation software, software application, software resource | Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer. | simulation, supercomputer, commodity cluster, gpu, parallel algorithm, biological system, parallel algorithms, computer, processor | is used by: CHARMM-GUI | Open source, Free for non-commercial use, Commercial entities must contact Schrodinger LLC | SCR_014575 | 2026-09-12 12:58:18 | 946 | ||||||||||
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BRAINS Imagebank Resource Report Resource Website 10+ mentions |
BRAINS Imagebank (RRID:SCR_014576) | data or information resource, database, image collection | A searchable collection of anonymised images and associated clinical data. It includes normal individuals at all ages (from prenatal to old age). The image bank contains integrated data sets already collected as part of research studies which include control subjects. New data is added as they become available. | database, image collection, brain, normal, control, human, integrated data set | is hosted by: University of Edinburgh; Scotland; United Kingdom | Registration required | SCR_014576 | Brain Images of Normal Subjects (BRAINS) Imagebank, Brain Images of Normal Subjects Imagebank | 2026-09-12 12:58:18 | 12 | |||||||||
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Odyssey CLx Resource Report Resource Website 100+ mentions |
Odyssey CLx (RRID:SCR_014579) | data analysis software, data processing software, software application, software resource | A data analysis software developed to simplify and record data from fluorescent related assays such as Western Blots, EMSAs, and Western Assays. This software will consolidate all of the resulting data into one easy-to-track image, and thus removes the need for multiple exposures, as well as standardizing the resulting fluorescent bands without image saturation, blowout, or removed sensitivity. Odyssey CLx is capable of scanning multiple mini-blots, microplates, or slides at the same time. | data analysis software, data processing software, fluorescence, software, band, image saturation, single image, western blot, emsa, western assay, image tracking, data simplification, sensitivity | has parent organization: LI-COR Biosciences | Commercial, Paired with a Scanning System | SCR_014579 | Odyssey CLx Imaging System | 2026-09-12 12:58:18 | 137 | |||||||||
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Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP Resource Report Resource Website |
Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP (RRID:SCR_014612) | software resource | An R-package which uses Dirichlet-Multinomial distribution to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments. | microbiome, r, hypothesis testing, human microbiome, dirichlet multinomial distribution | is listed by: Human Microbiome Project | SCR_014612 | 2026-09-12 12:58:19 | 0 | |||||||||||
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SitePainter Resource Report Resource Website 1+ mentions |
SitePainter (RRID:SCR_014618) | data processing software, data visualization software, software application, software resource, web application | An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context. | microbiome, microbial ecology, data visualization, desktop application | is listed by: Human Microbiome Project | Available for download | http://hmpdacc.org/sp/ | SCR_014618 | 2026-09-12 12:58:19 | 5 | |||||||||
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Unifrac Resource Report Resource Website 500+ mentions |
Unifrac (RRID:SCR_014616) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample. | microbiome, comparison, microbial community, phylogenetic tree, sequence | is listed by: Human Microbiome Project | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014616 | 2026-09-12 12:58:19 | 824 | ||||||||||
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Image Reader LAS-1000 Resource Report Resource Website 10+ mentions |
Image Reader LAS-1000 (RRID:SCR_014585) | data acquisition software, data processing software, software application, software resource | A software which is used to control the LAS-1000plus luminescent image analyzer. This software adjusts the focus, exposure time, sensitivity, and cooling temperature, and will record the data after the sample is scanned. | image analyzer, exposure, focus, sensitivity, cooling temperature, data, software | Commercial, Paired with a scanning system | SCR_014585 | 2026-09-12 12:58:18 | 45 | |||||||||||
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PowerChrom Resource Report Resource Website 50+ mentions |
PowerChrom (RRID:SCR_014588) | data acquisition software, data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. A software which collects, displays, and analyzes chromatographic signals. This software doesn't require any programming, and collects signals from one or two detectors. PowerChrom is supplied as part of the PowerChrom system, or separately for use with e-corder recording systems. | chromatography, chromatography data, no programming, e-corder, software, data acquisition, data analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014588 | 2026-09-12 12:58:19 | 97 | |||||||||||
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Metapath Resource Report Resource Website 10+ mentions |
Metapath (RRID:SCR_014621) | data analysis software, data processing software, software application, software resource | A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG. | microbiome, statistics, metagenomics, pathway, sequence, comaprison | is listed by: Human Microbiome Project | Available for download | SCR_014621 | 2026-09-12 12:58:19 | 19 | ||||||||||
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Vision Egg Resource Report Resource Website 10+ mentions |
Vision Egg (RRID:SCR_014589) | software library, software resource, software toolkit | A programming library that uses standard graphics cards to produce 2D and 3D visual stimuli for vision research experiments. | standard graphic, visual stimuli, vision research, software | is hosted by: GitHub | Open Source, Free, Source code is hosted on GitHub | SCR_014589 | 2026-09-12 12:58:19 | 16 | ||||||||||
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Open Targets Resource Report Resource Website 100+ mentions |
Open Targets (RRID:SCR_014622) | A public–private initiative that supports research that provides evidence on the biological validity of therapeutic targets and that gain insight into the effectiveness of pharmacological intervention. It aims to provide a research and development framework that applies human disease. It shares its information openly. | initiative, therapeutic, pharmacology, intervention, research and development, framework, man disease | is affiliated with: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | Open, Can interact with companies | http://www.ebi.ac.uk/about/news/press-releases/open-targets-new-name-new-data#annotations:B-esfHqUEeaXCGe7nJasQw | SCR_014622 | Centre for Therapeutic Target Validation, Center for Therapeutic Target Validation | 2026-09-12 12:58:19 | 143 | |||||||||
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Zeiss Axioskop Software Resource Report Resource Website 1+ mentions |
Zeiss Axioskop Software (RRID:SCR_014587) | data acquisition software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented January 19, 2022. Software used to control the Zeiss Axioskop microscope. | microscope, microscope software, zeiss, microscope management software, system management software | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014587 | 2026-09-12 12:58:19 | 9 | |||||||||||
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HUMAnN Resource Report Resource Website 500+ mentions |
HUMAnN (RRID:SCR_014620) | data processing software, software application, software resource, workflow software | A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities. | microbiome, dna reads, rna reads, workflow software, pipeline | is listed by: Human Microbiome Project | SCR_014620 | HMP Unified Metabolic Analysis Network (HUMAnN), HMP Unified Metabolic Analysis Network | 2026-09-12 12:58:19 | 507 |
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