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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-12 01:02:28 | 28 | |||||||
|
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 | 2026-09-12 01:02:26 | 1 | |||||
|
enviPick Resource Report Resource Website 1+ mentions |
enviPick (RRID:SCR_003059) | software resource, web site | Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_05010 | https://rdrr.io/cran/enviPick/ | SCR_003059 | enviPick: Peak picking for high resolution mass spectrometry data | 2026-09-12 01:02:29 | 2 | |||||||
|
flowFP Resource Report Resource Website 1+ mentions |
flowFP (RRID:SCR_001537) | software resource | A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956416 | Free, Available for download, Freely available | OMICS_05599 | SCR_001537 | flowFP - Fingerprinting for Flow Cytometry | 2026-09-12 12:55:27 | 4 | |||||||
|
MCMC.qpcr Resource Report Resource Website 10+ mentions |
MCMC.qpcr (RRID:SCR_001721) | software resource | Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977043 | Free, Available for download, Freely available | OMICS_03934 | SCR_001721 | MCMC.qpcr: Bayesian analysis of qRT-PCR data | 2026-09-12 12:55:30 | 24 | |||||||
|
plateCore Resource Report Resource Website |
plateCore (RRID:SCR_001743) | data or information resource, database, software resource | Software that provides basic S4 data structures and routines for analyzing plate based 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 |
PMID:19956418 | Free, Available for download, Freely available | OMICS_05641 | http://www.bioconductor.org/packages/release/bioc/html/plateCore.html | SCR_001743 | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-09-12 12:55:30 | 0 | ||||||
|
SLqPCR Resource Report Resource Website 10+ mentions |
SLqPCR (RRID:SCR_001669) | software resource | Software functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH. | standalone software, mac os x, unix/linux, windows, r, microtitre plate assay, qpcr |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_04010 | SCR_001669 | SLqPCR - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH | 2026-09-12 12:55:29 | 25 | ||||||||
|
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 | 2026-09-12 12:55:32 | 11 | ||||||
|
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 | 2026-09-12 12:55:31 | 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 | 2026-09-12 12:55:31 | 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 | 2026-09-12 12:55:33 | 7 | ||||||||
|
TagDust Resource Report Resource Website 50+ mentions |
TagDust (RRID:SCR_004175) | TagDust | software resource | A program to eliminate artifactual reads from next-generation sequencing data sets. | unix/linux, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:19737799 | biotools:tagdust, OMICS_01095, biotools:nexalign | https://bio.tools/tagdust, https://bio.tools/nexalign | SCR_004175 | 2026-09-12 12:56:10 | 55 | |||||||
|
Kdetrees Resource Report Resource Website |
Kdetrees (RRID:SCR_004522) | software resource | R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. | applet, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24764459 | GNU General Public License, v2 | biotools:kdetrees, OMICS_04172 | https://github.com/grady/kdetrees, https://bio.tools/kdetrees | SCR_004522 | kdetrees: Nonparametric method for identifying discordant phylogenetic trees | 2026-09-12 12:56:14 | 0 | ||||||
|
YuGene Resource Report Resource Website 10+ mentions |
YuGene (RRID:SCR_006023) | software resource | Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24667244 | GNU General Public License, v2, v3 | OMICS_04030 | SCR_006023 | YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses | 2026-09-12 12:56:34 | 16 | |||||||
|
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 | 2026-09-12 12:56:37 | 481 | |||||||
|
ABS filter Resource Report Resource Website |
ABS filter (RRID:SCR_005328) | ABS filter | software resource | R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. | unix/linux |
is listed by: OMICtools has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland |
PMID:24255646 | GNU General Public License, v3 | OMICS_00427 | SCR_005328 | R package - ABS filter, absfilter | 2026-09-12 12:56:24 | 0 | ||||||
|
aLFQ Resource Report Resource Website 10+ mentions |
aLFQ (RRID:SCR_005925) | software resource | An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24753486 | GNU General Public License, v3 or greater | OMICS_04053 | SCR_005925 | aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data | 2026-09-12 12:56:33 | 22 | |||||||
|
reseqtools Resource Report Resource Website 10+ mentions |
reseqtools (RRID:SCR_010806) | reseqtools | software resource | A Toolkit for analyzing next-generation DNA Re-Sequencing data. | java, unix/linux |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_00293 | SCR_010806 | 2026-09-12 12:57:23 | 18 | ||||||||
|
AliView Resource Report Resource Website 1000+ mentions |
AliView (RRID:SCR_002780) | software resource | Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets. | unix/linux, mac os x, windows, java | is listed by: OMICtools | PMID:25095880 | Free, Freely available | OMICS_05209 | http://www.ormbunkar.se/aliview/ | SCR_002780 | 2026-09-12 12:55:46 | 1039 | |||||||
|
NetPathMiner Resource Report Resource Website 1+ mentions |
NetPathMiner (RRID:SCR_002757) | software resource | Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths. | software package, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25075120 | Free, Freely available, Available for download | biotools:netpathminer, OMICS_05210 | https://bio.tools/netpathminer | SCR_002757 | NetPathMiner: R package for network path mining through gene expression | 2026-09-12 12:55:46 | 3 |
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