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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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R-package for adaptive fMRI analysis Resource Report Resource Website |
R-package for adaptive fMRI analysis (RRID:SCR_002530) | R-package for adaptive fMRI analysis | data processing software, image analysis software, image processing software, software application, software resource | The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155935 | SCR_002530 | 2026-09-05 06:29:55 | 0 | ||||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-05 06:30:00 | 1104 | |||||
|
CPRDLooksups.R Resource Report Resource Website |
CPRDLooksups.R (RRID:SCR_018959) | software application, software resource, text extraction software | Software R tool used to identify and retrieve CPRD clinical additional record information such as, smoking, weight/BMI, and medical tests. | Script, R, identify information, retrieve information, CPRD, clinical record information, smoking, weight, BMI, medical test, clinical data | Free, Freely available | SCR_018959 | 2026-09-05 06:32:16 | 0 | |||||||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-09-05 06:30:19 | 0 | ||||||
|
fastcluster Resource Report Resource Website |
fastcluster (RRID:SCR_023597) | software library, software resource, software toolkit | Software Python library for hierarchical clustering. Fast Hierarchical, Agglomerative Clustering Routines for R and Python. | Agglomerative clustering routines, R, Python, hierarchical clustering, | Free, Available for download, Freely available | http://danifold.net/fastcluster.html, https://packages.debian.org/search?keywords=python-fastcluster | SCR_023597 | 2026-09-05 06:30:24 | 0 | ||||||||||
|
clValid Resource Report Resource Website 50+ mentions |
clValid (RRID:SCR_014626) | data analysis software, data processing software, software application, software resource | An R package which contains functions for validating the results of a clustering analysis. | data analysis software, r, software package, cluster, cluster analysis, validation, results validation | is related to: CRAN | https://cran.r-project.org/web/packages/clValid/clValid.pdf | SCR_014626 | clValid - Validation of Clustering Results, clValid: Validation of Clustering Results | 2026-09-05 06:27:49 | 86 | |||||||||
|
CummeRbund Resource Report Resource Website 100+ mentions |
CummeRbund (RRID:SCR_014568) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions. | r software, cufflink, rna-seq, sqlite, gene, transcript, transcription start site, cds region, r, rnaseq, rna seq, bio.tools, FASEB list |
uses: R Project for Statistical Computing is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard University; Cambridge; United States |
Free, Freely available | biotools:cummerbund, OMICS_07349 | https://bio.tools/cummerbund, https://sources.debian.org/src/r-bioc-cummerbund/ | SCR_014568 | 2026-09-05 06:27:48 | 366 | ||||||||
|
ggplot2 Resource Report Resource Website 10000+ mentions |
ggplot2 (RRID:SCR_014601) | data processing software, data visualization software, software application, software resource | Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers. | plotting system, r, graphics, data analysis, multi-layered graphics, bio.tools |
uses: ggpubr uses: ggeffects uses: ggsignif is used by: riboWaltz is used by: ClustVis is used by: ggrepel is used by: PlotsOfData is used by: EnhancedVolcano is used by: tidyverse is used by: ComplexUpset is used by: ggfortify is used by: forestmodel is used by: ggvenn is used by: metaviz is used by: ggVennDiagram is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: ggraph is related to: ggbiplot is related to: GGally is related to: ggstatsplot is related to: ggpointdensity has parent organization: CRAN works with: Plotly works with: cowplot works with: ggalluvial works with: ggforce works with: ggbreak works with: ggrastr works with: tidybayes works with: ggsurvfit works with: ggtext works with: ggsci |
Free, Freely available | biotools:ggplot2 | http://docs.ggplot2.org/current/, https://github.com/tidyverse/ggplot2, https://bio.tools/ggplot2 | http://ggplot2.org/ | SCR_014601 | grammar of graphics plot2 | 2026-09-05 06:27:48 | 42192 | ||||||
|
HMPTrees Resource Report Resource Website |
HMPTrees (RRID:SCR_014613) | data analysis software, data processing software, software application, software resource | An R-package which uses Object Oriented Data Analysis (OODA) methods to analyze taxonomic trees directly, providing tools to model, compare, and visualize populations of taxonomic tree objects. | microbiome, r, taxonomic tree, rdp, statistical object oriented data | is listed by: Human Microbiome Project | SCR_014613 | Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data, HMPTrees - Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data | 2026-09-05 06:27:49 | 0 | ||||||||||
|
CTSgetR Resource Report Resource Website |
CTSgetR (RRID:SCR_014672) | software application, software resource, source code, systems interoperability software | R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers. | statistical analysis, statistical analysis package, r, r package, source code, system interoperability, software, translation, chemical, metabolomics | is listed by: Metabolomics Workbench | Freely available | SCR_014672 | 2026-09-05 06:27:49 | 0 | ||||||||||
|
survminer Resource Report Resource Website 100+ mentions |
survminer (RRID:SCR_021094) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package provides functions for facilitating survival analysis and visualization. | survival analysis, survival visualization, R | is related to: R Project for Statistical Computing | Free, Available for download, Freely available | SCR_021094 | 2026-09-05 06:29:34 | 133 | ||||||||||
|
rstatix Resource Report Resource Website 100+ mentions |
rstatix (RRID:SCR_021240) | data analytics software, software application, software resource, software toolkit | Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances. | Statistical tests, t-test, Wilcoxon test, ANOVA, Kruskal-Wallis, correlation analyses, R, visualization | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/kassambara/rstatix | SCR_021240 | 2026-09-05 06:29:37 | 133 | |||||||||
|
CAFE Resource Report Resource Website 500+ mentions |
CAFE (RRID:SCR_005983) | CAFE | software resource | R software package for the detection of gross chromosomal abnormalities from gene expression microarray data. | affymetrix, r, chromosomal abnormality, gene expression, microarray, chromosome, linux, windows |
is listed by: OMICtools has parent organization: Bitbucket |
PMID:24451624 | GNU General Public License, v3, Acknowledgement requested | OMICS_02245 | SCR_005983 | 2026-09-05 06:25:45 | 883 | |||||||
|
RUVSeq Resource Report Resource Website 100+ mentions |
RUVSeq (RRID:SCR_006263) | software resource | Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | software package, unix/linux, mac os x, windows, r, differential expression, preprocessing, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25150836 | Artistic License, v2 | OMICS_05652 | SCR_006263 | RUVSeq: Remove Unwanted Variation from RNA-Seq Data | 2026-09-05 06:25:49 | 481 | |||||||
|
AbsCN-seq Resource Report Resource Website 1+ mentions |
AbsCN-seq (RRID:SCR_006409) | AbsCN-seq | software resource | Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data. | r, statistics, purity, ploidy, absolute copy number, next-generation sequencing |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
Tumor, Cancer | PMID:24389661 | Free, Public | OMICS_02202 | SCR_006409 | 2026-09-05 06:25:53 | 7 | ||||||
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R package: Deducer Resource Report Resource Website 1+ mentions |
R package: Deducer (RRID:SCR_015659) | data analysis software, data processing software, software application, software resource | Data Analysis GUI for R. The program is based on Java's Swing GUI library and includes an Excel-like spreadsheet for easy data viewing and editing. | r, r package, statistical analysis, data viewing, data editing, spreadsheet, java, gui | Free, Available for download | SCR_015659 | Deducer, Deducer: A Data Analysis GUI for R | 2026-09-05 06:27:57 | 2 | ||||||||||
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braincog Resource Report Resource Website 1+ mentions |
braincog (RRID:SCR_015871) | data analysis software, data processing software, software application, software resource | Software package to elucidate complex interactions between subsets of neuroanatomical features and subsets of cognitive features. briancog specializes in differential correlation analysis. | r package, r, differential analysis, neuroanatomy, cognition | is related to: R Project for Statistical Computing | France-Stanford Center for Interdisciplinary Studies ; Swiss National Science Foundation |
DOI:10.1007/s12021-017-9351-z | Free, Available for download | SCR_015871 | 2026-09-05 06:28:00 | 3 | ||||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
Cancer Research UK A17197; European Molecular Biology Laboratory ; National Health and Medical Research Council of Australia APP1112681; Oxford Single Cell Biology Consortium ; United Kingdom Medical Research Council |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-09-05 06:28:01 | 187 | ||||||
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jamovi Resource Report Resource Website 1000+ mentions |
jamovi (RRID:SCR_016142) | data analysis software, data processing software, software application, software resource | Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience. | spreadsheet, r, statistic, methodology, r, package, analysis | Free, Available for download | SCR_016142 | the jamovi project | 2026-09-05 06:28:04 | 4164 | ||||||||||
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ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-09-05 06:33:22 | 35 |
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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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