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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software resource, software application, 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 |
NCI CA009363; NCI CA138249; NHGRI HG006853; Edelman-Gardner Foundation |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-08-03 09:31:28 | 1 | |||||
|
OrderedList Resource Report Resource Website 10+ mentions |
OrderedList (RRID:SCR_001834) | software resource | An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. | standalone software, mac os x, unix/linux, windows, r, differential expression, microarray, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16844712 | Free, Available for download, Freely available | OMICS_03525 | http://compdiag.molgen.mpg.de/software/OrderedList.shtml | SCR_001834 | OrderedList - Similarities of Ordered Gene Lists | 2026-08-01 12:02:04 | 11 | ||||||
|
R Project for Statistical Computing Resource Report Resource Website 10000+ mentions |
R Project for Statistical Computing (RRID:SCR_001905) | R | software resource | Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS. | R software, statistical, computing, graphics, programming, language, bio.tools |
is used by: UTR is used by: MSstats is used by: CummeRbund is used by: deFuse is used by: JASP is used by: Boruta is used by: NMRProcFlow is used by: PlotsOfData is used by: rtransparent is used by: shinyCircoss is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: CRAN is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is related to: Sweave is related to: rOpenSci is related to: R Manuals is related to: Bioconductor is related to: ggplot2 is related to: madsim is related to: Solas is related to: braincog is related to: clustree is related to: PhenoSpD is related to: geomorph is related to: NeuroAnatomy Toolbox is related to: dplyr is related to: glmmADMB is related to: clusterProfiler is related to: ropls is related to: mixOmics is related to: FlowSOM is related to: Rtsne is related to: scran is related to: Rsubread is related to: riboSeqR is related to: Biostrings is related to: riboWaltz is related to: GenomicFeatures is related to: devtools is related to: affy is related to: affydata is related to: Heatmapper is related to: toxprofileR is related to: LTRpred is related to: RaceID is related to: PRSice is related to: Genomic Ranges is related to: Goseq is related to: GAGE is related to: metagear is related to: pagoda2 is related to: dndSCV is related to: tidyr is related to: ClustVis is related to: IDR is related to: NeuroAnatomy Toolbox is related to: rjags is related to: gProfiler2 is related to: knitr is related to: EpiEstim is related to: Minimum-Hypergeometric Test is related to: Network-Based R-Statistics is related to: seqpac is related to: survminer is related to: Vector Generalized Linear and Additive Models is related to: LEA is related to: StAMPP is related to: Betareg is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: Rphenograph is related to: Peptides is related to: taxize is related to: seqinr is related to: reshape2 is related to: monaLisa is related to: mia is related to: Rtsne is related to: R package:stats-package is related to: R package: maxstat is related to: stats |
PMID:18252159 | SCR_021974, nif-0000-10474, OMICS_01147, biotools:r | https://cran.r-project.org/src/base/R-3/, https://bio.tools/r | SCR_001905 | R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing | 2026-08-01 12:02:06 | 47818 | ||||||
|
flowClust Resource Report Resource Website 10+ mentions |
flowClust (RRID:SCR_001807) | software resource | A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19442304 | Artistic License, v2 | OMICS_05595 | SCR_001807 | flowClust - Clustering for Flow Cytometry | 2026-08-01 12:02:03 | 15 | |||||||
|
COMPASS Resource Report Resource Website 1+ mentions |
COMPASS (RRID:SCR_001801) | software resource | Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:26006008 | Free, Available for download, Freely available | OMICS_05640 | SCR_001801 | Combinatorial Polyfunctionality Analysis of Single Cells, COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells, COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells | 2026-08-01 12:01:36 | 2 | |||||||
|
flowUtils Resource Report Resource Website 1+ mentions |
flowUtils (RRID:SCR_001879) | software resource | Software that provides utilities for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, decision tree, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05614 | SCR_001879 | flowUtils - Utilities for flow cytometry | 2026-08-01 12:01:38 | 6 | ||||||||
|
flowTrans Resource Report Resource Website 1+ mentions |
flowTrans (RRID:SCR_002093) | software resource | Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21050468 | Free, Available for download, Freely available | OMICS_05612 | SCR_002093 | flowTrans - Parameter Optimization for Flow Cytometry Data Transformation | 2026-08-01 12:01:59 | 4 | |||||||
|
flowMap Resource Report Resource Website 1+ mentions |
flowMap (RRID:SCR_002269) | software resource | Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process. | software package, mac os x, unix/linux, windows, r, flow cytometry, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_05600 | SCR_002269 | flowMap - A probabilistic algorithm for matching and comparing multiple flow cytometry samples | 2026-08-01 12:02:09 | 5 | ||||||||
|
shinyTANDEM Resource Report Resource Website |
shinyTANDEM (RRID:SCR_002169) | software resource | Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files. | mac os x, unix/linux, windows, r, mass spectrometry, proteomics |
uses: rTANDEM is listed by: OMICtools has parent organization: Bioconductor |
PMID:24700319 | Free, Available for download, Freely available | OMICS_03517 | http://www.bioconductor.org/packages/release/bioc/html/shinyTANDEM.html | http://www.bioconductor.org/packages/devel/bioc/html/shinyTANDEM.html, Resource:rTANDEM | SCR_002169 | 2026-08-01 12:02:08 | 0 | ||||||
|
flowMatch Resource Report Resource Website 1+ mentions |
flowMatch (RRID:SCR_002283) | software resource | Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22536861 | Free, Available for download, Freely available | OMICS_05602 | SCR_002283 | flowMatch - Matching and meta-clustering in flow cytometry | 2026-08-01 12:02:03 | 1 | |||||||
|
flowMeans Resource Report Resource Website 1+ mentions |
flowMeans (RRID:SCR_002275) | software resource | Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor is a plug in for: FlowJo |
PMID:21182178 | Artistic License, v2 | OMICS_05603 | SCR_002275 | flowMeans: Non-parametric Flow Cytometry Data Gating, flowMeans - Non-parametric Flow Cytometry Data Gating | 2026-08-01 12:02:09 | 6 | |||||||
|
flowMerge Resource Report Resource Website 1+ mentions |
flowMerge (RRID:SCR_002224) | software resource | Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20049161 | Free, Available for download, Freely available | OMICS_05605 | SCR_002224 | flowMerge - Cluster Merging for Flow Cytometry Data | 2026-08-01 12:02:08 | 2 | |||||||
|
flowPhyto Resource Report Resource Website |
flowPhyto (RRID:SCR_002183) | software resource | An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data. | software package, mac os x, unix/linux, windows, r, classification, clustering, data import, flow cytometry, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21208987 | Free, Available for download, Freely available | OMICS_05606 | http://www.bioconductor.org/packages/release/bioc/html/flowPhyto.html | SCR_002183 | flowPhyto - Methods for Continuous Flow Cytometry | 2026-08-01 12:01:43 | 0 | ||||||
|
BEAT Resource Report Resource Website 100+ mentions |
BEAT (RRID:SCR_002387) | software resource | Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data. | standalone software, unix/linux, mac os x, windows, r, dna methylation, epigenetics, genetics, methyl-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24618468 | GNU Lesser General Public License, v3 or greater | OMICS_03425 | SCR_002387 | BS-Seq Epimutation Analysis Toolkit, BEAT - BS-Seq Epimutation Analysis Toolkit | 2026-08-01 12:01:47 | 126 | |||||||
|
CAMERA - Collection of annotation related methods for mass spectrometry data Resource Report Resource Website 1+ mentions |
CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) | CAMERA | software resource | A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. | standalone software, mac os x, unix/linux, windows, r, spectra, extraction, annotation, liquid chromatography, mass spectrometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22111785 | Free, Available for download, Freely available | biotools:camera, OMICS_03366 | https://bio.tools/camera | SCR_002466 | CAMERA - Collection of annotation related methods for mass spectrometry data | 2026-08-01 12:02:10 | 4 | |||||
|
MethylAid Resource Report Resource Website 50+ mentions |
MethylAid (RRID:SCR_002659) | software resource | Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored. | software package, illumina, mac os x, unix/linux, windows, r, dna methylation, gui, methylation array, microarray, quality control, two channel, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25147358 | Free, Available for download, Freely available | biotools:methylaid, OMICS_05457 | http://www.bioconductor.org/packages/release/bioc/html/MethylAid.html, http://shiny.bioexp.nl/MethylAid/, https://bio.tools/methylaid | SCR_002659 | MethylAid - Visual and interactive quality control of large Illumina 450k data sets, MethylAid: Visual and interactive quality control of large Illumina 450k data sets | 2026-08-01 12:01:52 | 65 | ||||||
|
NormqPCR Resource Report Resource Website 50+ mentions |
NormqPCR (RRID:SCR_003388) | NormqPCR | software resource | Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data. | gene expression, microtitre plate assay, qpcr, reference gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22748112 | Free, Available for download, Freely available | OMICS_02315, biotools:normqpcr | https://bio.tools/normqpcr | SCR_003388 | NormqPCR - Functions for normalisation of RT-qPCR data | 2026-08-01 12:02:20 | 51 | |||||
|
SWAN Resource Report Resource Website 100+ mentions |
SWAN (RRID:SCR_003455) | SWAN | software resource | Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package. | dna methylation, microarray |
is listed by: OMICtools is related to: minfi has parent organization: Bioconductor |
PMID:22703947 | Free, Available for download, Freely available | OMICS_02303 | SCR_003455 | Subset-quantile Within Array Normalization | 2026-08-01 12:02:21 | 190 | ||||||
|
DEGseq Resource Report Resource Website 1000+ mentions |
DEGseq (RRID:SCR_008480) | DEGseq | software resource | R package to identify differentially expressed genes from RNA-Seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01305 | SCR_008480 | 2026-08-01 12:03:45 | 1643 | ||||||||||
|
DeconRNASeq Resource Report Resource Website 10+ mentions |
DeconRNASeq (RRID:SCR_006713) | DeconRNASeq | software resource | An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01230 | SCR_006713 | 2026-08-01 12:03:18 | 39 |
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