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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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iBMQ Resource Report Resource Website |
iBMQ (RRID:SCR_000481) | software resource | Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently. | standalone software, mac os x, unix/linux, windows, r, gene expression, microarray, preprocessing, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23958729 | Free, Available for download, Freely available | OMICS_04601 | SCR_000481 | iBMQ - integrated Bayesian Modeling of eQTL data | 2026-09-12 12:55:10 | 0 | |||||||
|
Simulx Resource Report Resource Website 1+ mentions |
Simulx (RRID:SCR_000486) | Simulx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator. | windows, linux, macos, model, r, simulation, population, covariate, dose regimen |
is related to: PharmML has parent organization: DDMoRe has parent organization: National Institute for Research in Computer Science and Control; Brittany; France |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158166 | SCR_000486 | 2026-09-12 12:55:10 | 2 | ||||||||
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fourSig Resource Report Resource Website |
fourSig (RRID:SCR_000516) | software resource | A suite of software programs for analyzing and visualizing 4C-seq data. | standalone software, perl, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24561615 | Free, Available for download, Freely available | OMICS_02628 | SCR_000516 | 2026-09-12 12:55:11 | 0 | ||||||||
|
GeneExpressionSignature Resource Report Resource Website 1+ mentions |
GeneExpressionSignature (RRID:SCR_000455) | software resource | An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest. | software package, r, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23374109 | Free, Available for download, Freely available | OMICS_04919 | SCR_000455 | GeneExpressionSignature - Gene Expression Signature based Similarity Metric | 2026-09-12 12:55:09 | 1 | |||||||
|
flowQ Resource Report Resource Website |
flowQ (RRID:SCR_000575) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05805 | SCR_000575 | flowQ: Quality control for flow cytometry | 2026-09-12 12:55:11 | 0 | ||||||||
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SigFuge Resource Report Resource Website |
SigFuge (RRID:SCR_000444) | software resource | Algorithm for testing significance of clustering in RNA-seq data. | software package, unix/linux, mac os x, windows, r, clustering, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25030904 | Free, Available for download, Freely available | OMICS_05201 | SCR_000444 | 2026-09-12 12:55:09 | 0 | ||||||||
|
DiMO Resource Report Resource Website 1+ mentions |
DiMO (RRID:SCR_001168) | DiMO | software resource | Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. | r, motif, perceptron |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:24369152 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02190 | SCR_001168 | Discriminative Motif Optimizer, DiMO: Discriminative Motif Optimizer | 2026-09-12 12:55:20 | 1 | ||||||
|
ExomePeak Resource Report Resource Website 1+ mentions |
ExomePeak (RRID:SCR_001076) | exomePeak | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. | r, matlab |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Texas at San Antonio; Texas; USA |
PMID:23589649 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00570 | SCR_001076 | 2026-09-12 12:55:18 | 5 | |||||||
|
Starr Resource Report Resource Website |
Starr (RRID:SCR_001071) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences. | data import, quality, visualization, r, genomics, mapping, data analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20398407 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00811 | SCR_001071 | 2026-09-12 12:55:18 | 0 | ||||||||
|
DSGseq Resource Report Resource Website |
DSGseq (RRID:SCR_001104) | DSGseq | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. R software program for identifying differentially spliced genes from two groups of RNA-seq samples. It reads the count file and outputs the differences in the relative abundance of the isoforms of each gene in the annotation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rna seq, isoform, genes, spliced genes, r, genomics, sequence analysis software | is listed by: OMICtools | PMID:23228854 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01331 | SCR_001104 | 2026-09-12 12:55:19 | 0 | |||||||
|
targetscan.Hs.eg.db Resource Report Resource Website |
targetscan.Hs.eg.db (RRID:SCR_001068) | data analysis software, data processing software, sequence analysis software, software application, software resource | R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. | software, biological targets, mirna, prediction, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00790 | SCR_001068 | 2026-09-12 12:55:18 | 0 | |||||||||
|
rGADEM Resource Report Resource Website |
rGADEM (RRID:SCR_001091) | data analysis software, data processing software, sequence analysis software, software application, software resource | R package with tools for de novo motif discovery in large-scale genomic sequence data. | de novo motif, genomics, sequencing, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00491 | SCR_001091 | 2026-09-12 12:55:19 | 0 | |||||||||
|
flowWorkspace Resource Report Resource Website 1+ mentions |
flowWorkspace (RRID:SCR_001155) | software resource | Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis. | software package, mac os x, unix/linux, windows, r, data import, data representation, flow cytometry, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | Free, Available for download, Freely available | OMICS_05616 | SCR_001155 | flowWorkspace - Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore | 2026-09-12 12:55:20 | 3 | |||||||
|
Patchwork Resource Report Resource Website 10+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | 2026-09-12 12:55:02 | 10 | |||||
|
R Manuals Resource Report Resource Website 1+ mentions |
R Manuals (RRID:SCR_000036) | R Manuals | data or information resource, narrative resource, training material | Manuals for R created on Debian Linux that can be downloaded as PDF files, EPUB files (for R-devel and R-patched), or directly browsed as HTML. They may differ from the manuals for Mac or Windows on platform-specific pages, but most parts will be identical for all platforms. | r, programming language, statistical analysis, graphics | is related to: R Project for Statistical Computing | Free, Available for download, Freely available | OMICS_01764 | SCR_000036 | The R Manuals | 2026-09-12 12:55:01 | 8 | |||||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | CorMut - Detect the correlated mutations based on selection pressure | 2026-09-12 12:55:02 | 0 | ||||||
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flowBin Resource Report Resource Website |
flowBin (RRID:SCR_000051) | software resource | A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers. | software package, flow cytometry data, r, cell based assay, expression |
is related to: CRAN has parent organization: Bioconductor has parent organization: BC Cancer Agency |
Canadian Cancer Society ; International Society for the Advancement of Cytometry ; Michael Smith Foundation for Health Research ; NIBIB R01EB008400 |
PMID:25600947 | Free, Available for download, Freely available | OMICS_05593 | SCR_000051 | flowBin - Combining multitube flow cytometry data by binning | 2026-09-12 12:55:02 | 0 | ||||||
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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 | 2026-09-12 12:58:19 | 86 | |||||||||
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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 | 2026-09-12 12:58:18 | 366 | ||||||||
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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 | 2026-09-12 12:58:19 | 42192 |
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