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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-09-05 06:27:49 | 0 | |||||||||||
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Hierarchical Clustering Resource Report Resource Website 1+ mentions |
Hierarchical Clustering (RRID:SCR_014673) | data analysis software, data processing software, software application, software resource, source code | R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method. | statistical analysis, statistical analysis package, r, r package, data analysis, software, cluster, hierarchical, dissimilarity, clustering method, metabolomics | is listed by: Metabolomics Workbench | Acknowledgement requested | SCR_014673 | R: Hierarchical Clustering, R - Hierarchical Clustering | 2026-09-05 06:27:49 | 4 | |||||||||
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Zeitzeiger Resource Report Resource Website 10+ mentions |
Zeitzeiger (RRID:SCR_014791) | data acquisition software, data processing software, software application, software resource | R package for regularized supervised learning on high-dimensional data from an oscillatory system. Zeitzeiger can quantify rhythmic behavior, make accurate predictions, identify major patterns and important features, and detect when the oscillator is perturbed. | r, data acquisition software, rhythm, behavior, predict, oscillatory system, high dimensional data, regularized supervised learning | Available for download | SCR_014791 | ZeitZeiger | 2026-09-05 06:27:51 | 13 | ||||||||||
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Principal Components Analysis Resource Report Resource Website 10+ mentions |
Principal Components Analysis (RRID:SCR_014676) | data analysis software, data processing software, software application, software resource, source code | R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp. | statistical analysis, statistical analysis package, r, r package, principal component analysis, data matrix, prcomp, metabolomics | is listed by: Metabolomics Workbench | SCR_014676 | 2026-09-05 06:27:49 | 17 | |||||||||||
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Linear Discriminant Analysis Resource Report Resource Website |
Linear Discriminant Analysis (RRID:SCR_014675) | data analysis software, data processing software, software application, software resource, source code | R documentation for a function to perform linear discriminant analysis; specifically, to detect if the within-class covariance matrix is singular. | statistical analysis, statistical analysis package, r, r package, linear disciminant analysis, covariance, matrix, linear discriminant analysis, data analysis software, metabolomics | is listed by: Metabolomics Workbench | SCR_014675 | 2026-09-05 06:27:49 | 0 | |||||||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | data analysis software, data processing software, software application, software resource, source code | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-09-05 06:27:58 | 1808 | |||||
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R package: LMERConvenienceFunctions Resource Report Resource Website 1+ mentions |
R package: LMERConvenienceFunctions (RRID:SCR_015658) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software package that performs backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. | r, fixed effect, random effect, anova, p-value, r-squared, data trimming, data visualization | is listed by: CRAN | Free, Available for download | SCR_015658 | LMERConvenienceFunctions, Package ‘LMERConvenienceFunctions’, LMERConvenienceFunctions: Model Selection and Post-hoc Analysis for (G)LMER Models | 2026-09-05 06:27:57 | 5 | |||||||||
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R package: lattice Resource Report Resource Website 10+ mentions |
R package: lattice (RRID:SCR_015662) | data processing software, data visualization software, software application, software resource | Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements. | r, r package, multivariate data, data visualization | is listed by: CRAN | Free, Available for download | SCR_015662 | lattice, lattice: Trellis Graphics for R, Package ‘lattice’ | 2026-09-05 06:27:57 | 13 | |||||||||
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NAPR: Neuroanatomical Age Prediction using R Resource Report Resource Website 1+ mentions |
NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) | NAPR | data repository, service resource, storage service resource | Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3. | neuroanatomy, prediction, r, neuroimaging, mri scan, cortical thickness, relevance vector | DOI:10.1101/099309 | Free, Available for download | http://www.cloudneuro.org/ | SCR_015759 | Neuroanatomical Age Prediction using R | 2026-09-05 06:27:59 | 1 | |||||||
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statsmodel Resource Report Resource Website 100+ mentions |
statsmodel (RRID:SCR_016074) | data analysis software, data processing software, software application, software resource | Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html | python, statistic, estimate, econometric, model, library, class, function, r | Open source, Available for download | SCR_016074 | Statsmodels: Econometric and Statistical Modeling with Python | 2026-09-05 06:28:03 | 253 | ||||||||||
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HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NIGMS R01 ; NIH R01 AI47745; NIH U01 AI43638; NSF DBI-0096033; NSF DEB-9996118; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/, https://veg.github.io/hyphy-site/, https://github.com/veg/hyphy, https://bio.tools/HyPhy, | SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-09-05 06:28:04 | 1586 | |||||
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zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:04 | 128 | ||||||
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GC/GCF Resource Report Resource Website 1+ mentions |
GC/GCF (RRID:SCR_009075) | software application, software resource | Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, linux | is listed by: Genetic Analysis Software | SCR_000846, nlx_154072, nlx_154584 | SCR_009075 | R/GCF, R/GC, Genomic Control | 2026-09-05 06:31:55 | 1 | |||||||||
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COVIBD Resource Report Resource Website |
COVIBD (RRID:SCR_009155) | software application, software resource | Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154207, SCR_009109, nlx_154275 | SCR_009155 | R/COVIBD | 2026-09-05 06:31:55 | 0 | |||||||||
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metaMA Resource Report Resource Website |
metaMA (RRID:SCR_000408) | software resource, software toolkit | Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: CRAN is related to: SMAGEXP |
Scottish Government Rural and Environment Research and Analysis Directorate | PMID:19628502 | Free, Available for download, Freely available | OMICS_03524 | SCR_000408 | Meta-analysis for MicroArrays, Meta analysis for MicroArrays | 2026-09-05 06:32:21 | 0 | ||||||
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ADEGENET Resource Report Resource Website 10+ mentions Issue |
ADEGENET (RRID:SCR_000825) | ADEGENET | software application, software resource | Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, r |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:21926124 PMID:18397895 DOI:10.1093/bioinformatics/btn129 |
Free, Available for download, Freely available | nlx_153996, nlx_154580, OMICS_11078, SCR_007239 | http://adegenet.r-forge.r-project.org/, https://sources.debian.org/src/r-cran-adegenet/ | SCR_000825 | R/ADEGENET | 2026-09-05 06:32:22 | 22 | |||||
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VennDiagram Resource Report Resource Website 1000+ mentions |
VennDiagram (RRID:SCR_002414) | software resource, software toolkit | Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. | Venn and Euler plots, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: Debian is related to: jVenn has parent organization: CRAN |
PMID:21269502 | Free, Available for download, Freely available | OMICS_05570 | https://sources.debian.org/src/r-cran-venndiagram/ | SCR_002414 | VennDiagram: Generate high-resolution Venn and Euler plots | 2026-09-05 06:32:26 | 2138 | ||||||
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MUMA Resource Report Resource Website 10+ mentions |
MUMA (RRID:SCR_002412) | MUMA | software application, software resource, standalone software | Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY). | standalone software, mac os x, unix/linux, windows, r, metabolomics, univariate, multivariate, data analysis |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_03370 | SCR_002412 | Metabolomics Univariate and Multivariate Analysis (MUMA), Metabolomic Univariate and Multivariate Analysis | 2026-09-05 06:32:26 | 28 | |||||||
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nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, software resource, standalone software | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Edelman-Gardner Foundation ; NCI CA009363; NCI CA138249; NHGRI HG006853 |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-09-05 06:32:25 | 1 | |||||
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cortex Resource Report Resource Website 100+ mentions |
cortex (RRID:SCR_002467) | cortex | software application, software resource | Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | clinical neuroinformatics, mgh/mgz, magnetic resonance, r, surface analysis, thickness, mri, cortical thickness, morphometry, neuroimaging, power analysis, study design, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: bio.tools is listed by: Debian has parent organization: Brain Research Institute |
PMID:22807270 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155842, biotools:cortex | http://brain.org.au/software/cortex/power, http://www.nitrc.org/projects/cortex, https://bio.tools/cortex | SCR_002467 | Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies | 2026-09-05 06:32:27 | 374 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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