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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-08-08 12:00:33 | 9083 | |||||||
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SigmaGel Software Resource Report Resource Website 100+ mentions |
SigmaGel Software (RRID:SCR_014598) | software resource, software application, data analysis software, data processing software | Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images. | gel, gel analysis software, twain, data analysis | Available from SPSS Software | SCR_014598 | SigmaGel | 2026-08-08 12:00:14 | 151 | ||||||||||
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Stopwatch+ Resource Report Resource Website 10+ mentions |
Stopwatch+ (RRID:SCR_014591) | data acquisition software, software resource, software application, data processing software | A software which tracks the number of occurrences and duration of up to 16 defined events. The user can group events together so that turning on one event in a group will automatically turn off other active events in the group. Sessions can end after a fixed length of time, or the sessions can be ended manually, At the end of the session, the data can be saved in a comma-delimited file which can be easily imported into a spreadsheet application. | software, track events, occurences, auto-end, manual end, comma-delimited, spreadsheet | Open Source | SCR_014591 | Stopwatch plus, Stopwatch Plus, Stopwatch-plus | 2026-08-08 12:00:33 | 20 | ||||||||||
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StatPlus Mac Resource Report Resource Website 100+ mentions |
StatPlus Mac (RRID:SCR_014635) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:15 | 195 | ||||||||||
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CopyCaller Resource Report Resource Website 100+ mentions |
CopyCaller (RRID:SCR_014486) | software resource, software application, data analysis software, data processing software | A software for analyzing real-time PCR data and quantifying DNA targets. It can perform copy number analysis, report confidence in copy number, display data in table and graphic format, change analysis parameters, and view data analysis information for multiple experiments at once. | data analysis, real-time pcr data analysis, real-time pcr, pcr, dna target | SCR_014486 | 2026-08-08 12:00:25 | 344 | ||||||||||||
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Minitab Resource Report Resource Website 5000+ mentions |
Minitab (RRID:SCR_014483) | software resource, software application, data analysis software, data processing software | A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment. | data analysis, statistical analysis, hypothesis, confidence, descriptive | is listed by: SoftCite | SCR_014483 | 2026-08-08 12:00:25 | 6109 | |||||||||||
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BD CellQuest Pro Resource Report Resource Website 1000+ mentions |
BD CellQuest Pro (RRID:SCR_014489) | data acquisition software, software resource, software application, data processing software | 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 | 2026-08-08 12:00:25 | 3939 | |||||||||||
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BayesTraits Resource Report Resource Website 100+ mentions |
BayesTraits (RRID:SCR_014487) | software resource, software application, data analysis software, data processing software | A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. It incorporates earlier programs including Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a discrete number of states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and correlations among pairs of traits., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, evolution, phylogeny, evolutionary model | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014487 | 2026-08-08 12:00:31 | 308 | |||||||||||
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Clone Manager Software Resource Report Resource Website 10+ mentions |
Clone Manager Software (RRID:SCR_014521) | workflow software, software resource, software application, simulation software, data processing 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 | 2026-08-08 12:00:12 | 49 | |||||||||||
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Clickjoint Resource Report Resource Website 1+ mentions |
Clickjoint (RRID:SCR_014482) | software resource, software application, data analysis software, data processing software | A software for analyzing animal movement on videos and images. The user can define the animal's joints so the software can analyze using a tracking algorithm. | image analysis, tracking algorithm, animal movement, animal joint | SCR_014482 | 2026-08-08 12:00:11 | 3 | ||||||||||||
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Core Gene Evaluation Script Resource Report Resource Website 1+ mentions |
Core Gene Evaluation Script (RRID:SCR_014604) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:14 | 6 | ||||||||||
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inVUE Resource Report Resource Website 1+ mentions |
inVUE (RRID:SCR_014608) | software resource, software application, data analysis software, data visualization software, data processing software | 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 | 2026-08-08 12:00:27 | 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 | 2026-08-08 12:00:33 | 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, software resource, software application, data processing software | 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 | 2026-08-08 12:00:26 | 72 | |||||||||||
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Desmond Resource Report Resource Website 500+ mentions |
Desmond (RRID:SCR_014575) | software resource, software application, simulation software | 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 | 2026-08-08 12:00:32 | 946 | ||||||||||
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BRAINS Imagebank Resource Report Resource Website 10+ mentions |
BRAINS Imagebank (RRID:SCR_014576) | database, data or information resource, 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 | 2026-08-08 12:00:13 | 12 | |||||||||
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Odyssey CLx Resource Report Resource Website 100+ mentions |
Odyssey CLx (RRID:SCR_014579) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:26 | 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 | 2026-08-08 12:00:27 | 0 | |||||||||||
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SitePainter Resource Report Resource Website 1+ mentions |
SitePainter (RRID:SCR_014618) | web application, software resource, software application, data visualization software, data processing software | 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 | 2026-08-08 12:00:27 | 5 | |||||||||
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Unifrac Resource Report Resource Website 500+ mentions |
Unifrac (RRID:SCR_014616) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:33 | 824 |
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