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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NNcon Resource Report Resource Website 1+ mentions |
NNcon (RRID:SCR_014292) | prediction, software tool | Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. | text mining objective, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:19420062 | biotools:nncon | https://bio.tools/nncon | http://casp.rnet.missouri.edu/nncon.html | SCR_014292 | 2026-08-17 09:34:58 | 2 | |||||||
|
AnimalTracker Resource Report Resource Website 10+ mentions |
AnimalTracker (RRID:SCR_014397) | data processing software, software resource, data analysis software, software application | A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation. | animal, tracking system, universal, animal behavior, analysis | Hungarian Brain Research Program | Acknowledgment required, Available for download, Open source | SCR_014397 | Animal Tracker | 2026-08-17 09:35:00 | 22 | |||||||||
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StepOne Software Resource Report Resource Website 100+ mentions |
StepOne Software (RRID:SCR_014281) | data processing software, software resource, data analysis software, software application | A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data. | applied biosystems step one, pcr, data analysis software, instrument management software, experimental control | Pay for product | https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/StepOne-and-StepOnePlus-Real-Time-PCR-System.html | SCR_014281 | 2026-08-17 09:34:58 | 269 | ||||||||||
|
Mercator Resource Report Resource Website 500+ mentions |
Mercator (RRID:SCR_014493) | data processing software, software resource, data analysis software, software application | A software package for quantification of histological sections. This software performs functions including: management and analysis of regions of interest, annotations, statistical analysis, and 3D visualization. These results are edited in an Excel-compatible spreadsheet. | histology analysis, image analysis, statistical analysis, 3d visualization, excel | Commercial | SCR_014493 | 2026-08-17 09:35:01 | 692 | |||||||||||
|
Eelbrain Resource Report Resource Website 10+ mentions |
Eelbrain (RRID:SCR_014661) | data processing software, software resource, data analysis software, software application | Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases. | statistical analysis, analysis toolbox, electrical brain activity, meg, eeg | is hosted by: GitHub | NYU Abu Dhabi Institute G1001 | Open source, Acknowledgement requested | https://github.com/christianbrodbeck/Eelbrain | SCR_014661 | 2026-08-17 09:35:04 | 14 | ||||||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data processing software, software resource, data analysis software, software application | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-08-17 09:35:04 | 3874 | |||||
|
SigmaGel Software Resource Report Resource Website 100+ mentions |
SigmaGel Software (RRID:SCR_014598) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:03 | 151 | ||||||||||
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StatPlus Mac Resource Report Resource Website 100+ mentions |
StatPlus Mac (RRID:SCR_014635) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:04 | 195 | ||||||||||
|
CopyCaller Resource Report Resource Website 100+ mentions |
CopyCaller (RRID:SCR_014486) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:01 | 344 | ||||||||||||
|
Minitab Resource Report Resource Website 5000+ mentions |
Minitab (RRID:SCR_014483) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:01 | 6109 | |||||||||||
|
BayesTraits Resource Report Resource Website 100+ mentions |
BayesTraits (RRID:SCR_014487) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:01 | 308 | |||||||||||
|
Clickjoint Resource Report Resource Website 1+ mentions |
Clickjoint (RRID:SCR_014482) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:02 | 3 | ||||||||||||
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Core Gene Evaluation Script Resource Report Resource Website 1+ mentions |
Core Gene Evaluation Script (RRID:SCR_014604) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:03 | 6 | ||||||||||
|
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 | 2026-08-17 09:35:03 | 1198 | ||||
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Odyssey CLx Resource Report Resource Website 100+ mentions |
Odyssey CLx (RRID:SCR_014579) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:03 | 137 | |||||||||
|
Unifrac Resource Report Resource Website 500+ mentions |
Unifrac (RRID:SCR_014616) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:03 | 824 | ||||||||||
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Metapath Resource Report Resource Website 10+ mentions |
Metapath (RRID:SCR_014621) | data processing software, software resource, data analysis software, software application | 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 | 2026-08-17 09:35:04 | 19 | ||||||||||
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ABCDreport Resource Report Resource Website |
ABCDreport (RRID:SCR_016030) | data processing software, software resource, data analysis software, software application | Software application as a simple system to review study progress. Used in ABCD study. | system, simple, review, study, progress, development, adolescence, brain, cognitive, report | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016030 | 2026-08-17 09:35:34 | 0 | |||||||||
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zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | data processing software, software resource, data analysis software, software application | Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information. | single-cell, RNA-seq, UMI, Genomics, shell, r, perl, rna, cdna, cell, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/153940 | Open source, Free, Available for download | biotools:zumis | https://bio.tools/zumis | SCR_016139 | zumi | 2026-08-17 09:35:37 | 128 | ||||||
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GraPhlAn Resource Report Resource Website 100+ mentions |
GraPhlAn (RRID:SCR_016130) | data processing software, software resource, data visualization software, software application | Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | circular, high, resolution, microbal, tree, taxonomy, annotation, phylogenetic, investigation |
is listed by: Debian is listed by: OMICtools has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11549 | https://huttenhower.sph.harvard.edu/graphlan, https://sources.debian.org/src/graphlan/ | SCR_016130 | Graphlan | 2026-08-17 09:35:30 | 186 |
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