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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | SciCrunch Registry | Mfuzz - Soft clustering of time series gene expression data | 2026-10-31 12:12:39 | 16 | |||||
|
Rdisop Resource Report Resource Website |
Rdisop (RRID:SCR_000453) | software resource | Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02416, biotools:rdisop | https://github.com/sneumann/Rdisop, https://bio.tools/rdisop | SCR_000453 | SciCrunch Registry | Rdisop - Decomposition of Isotopic Patterns, Rdisop: Decomposition of Isotopic Patterns, Decomposition of Isotopic Patterns | 2026-10-31 12:12:38 | 0 | |||||||
|
FlipFlop Resource Report Resource Website |
FlipFlop (RRID:SCR_000625) | software resource | Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. | standalone software, unix/linux, mac os x, windows, r, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24813214 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04028, biotools:flipflop | https://bio.tools/flipflop | SCR_000625 | SciCrunch Registry | flipflop - Fast lasso-based isoform prediction as a flow problem | 2026-10-31 12:12:40 | 0 | ||||||
|
bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | data analysis software, data processing software, sequence analysis software, software application, software resource | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | SciCrunch Registry | bsseq - Analyze manage and store bisulfite sequencing data | 2026-10-31 12:12:45 | 8 | |||||||
|
MmPalateMiRNA Resource Report Resource Website 1+ mentions |
MmPalateMiRNA (RRID:SCR_001070) | data analysis software, data processing software, software application, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data. | murine, palate, mirna, two color expression, open source, r |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:23298515 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00788 | SCR_001070 | SciCrunch Registry | 2026-10-31 12:12:45 | 1 | ||||||||
|
R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | SciCrunch Registry | 2026-10-31 12:12:46 | 4 | ||||||||
|
RmiR Resource Report Resource Website |
RmiR (RRID:SCR_001069) | RmiR | data analysis software, data processing software, sequence analysis software, software application, software resource | R package that contains functions to merge microRNA and respective targets using different databases. | micro rna, mrna, function, target, r, sequence analysis software |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00789 | https://rdrr.io/bioc/RmiR/ | SCR_001069 | SciCrunch Registry | 2026-10-31 12:12:45 | 0 | |||||||
|
Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | data analysis software, data processing software, sequence analysis software, software application, software resource | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | SciCrunch Registry | 2026-10-31 12:12:45 | 0 | |||||||||
|
massiR Resource Report Resource Website |
massiR (RRID:SCR_001157) | software resource | Software that predicts the sex of samples in gene expression microarray datasets. | standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24659105 | Free, Available for download, Freely available | biotools:massir, OMICS_03638 | https://bio.tools/massir | SCR_001157 | SciCrunch Registry | massiR: MicroArray Sample Sex Identifier, MicroArray Sample Sex Identifier | 2026-10-31 12:12:46 | 0 | ||||||
|
sRAP Resource Report Resource Website 10+ mentions |
sRAP (RRID:SCR_001297) | sRAP | software resource | Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data. | gene expression, differential expression, go, gene set enrichment, microarray, preprocessing, quality control, rna-seq, statistical method, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02038 | http://www.bioconductor.org/packages/release/bioc/html/sRAP.html | SCR_001297 | SciCrunch Registry | Simplified RNA-Seq Analysis | 2026-10-31 12:12:49 | 16 | ||||||
|
yaqcaffy Resource Report Resource Website 1+ mentions |
yaqcaffy (RRID:SCR_001295) | yaqcaffy | software resource | Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. | microarray, one channel, quality control, report writing, affymetrix, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | BioTools:yaqcaffy, biotools:yaqcaffy, OMICS_02040 | http://www.bioconductor.org/packages/release/bioc/html/yaqcaffy.html | SCR_001295 | SciCrunch Registry | yaqcaffy - Affymetrix expression data quality control and reproducibility analysis | 2026-10-31 12:12:49 | 3 | ||||||
|
SNM Resource Report Resource Website 1+ mentions |
SNM (RRID:SCR_001299) | SNM | software resource | Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest. | differential expression, exon array, gene expression, microarray, multi channel, multiple comparison, one channel, preprocessing, quality control, transcription, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02036 | SCR_001299 | SciCrunch Registry | Supervised Normalization of Microarrays | 2026-10-31 12:12:49 | 1 | |||||||
|
ChIPsim Resource Report Resource Website 1+ mentions |
ChIPsim (RRID:SCR_001293) | ChIPsim | software resource | Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. | chip-seq, infrastructure, simulation |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_02042 | SCR_001293 | SciCrunch Registry | ChIPsim - Simulation of ChIP-seq experiments | 2026-10-31 12:12:49 | 1 | |||||||
|
methyAnalysis Resource Report Resource Website 1+ mentions |
methyAnalysis (RRID:SCR_001290) | methyAnalysis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data. | dna methylation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21159174 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02046 | SCR_001290 | SciCrunch Registry | methyAnalysis - DNA methylation data analysis and visualization | 2026-10-31 12:12:49 | 9 | ||||||
|
les Resource Report Resource Website |
les (RRID:SCR_001291) | les | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. | loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:les, OMICS_02045 | https://bioconductor.org/packages/les/, https://bio.tools/les | SCR_001291 | SciCrunch Registry | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-10-31 12:12:49 | 0 | ||||||
|
beadarraySNP Resource Report Resource Website |
beadarraySNP (RRID:SCR_001281) | beadarraySNP | software resource | Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports. | copy number variation, data import, genetic variability, preprocessing, snp, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02056 | http://www.bioconductor.org/packages/devel/bioc/html/beadarraySNP.html | SCR_001281 | SciCrunch Registry | beadarraySNP - Normalization and reporting of Illumina SNP bead arrays | 2026-10-31 12:12:48 | 0 | ||||||
|
RCASPAR Resource Report Resource Website |
RCASPAR (RRID:SCR_001253) | RCASPAR | software resource | Software package for survival time prediction based on a piecewise baseline hazard Cox regression model. It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. | gene expression, genetics, proteomics, visualization, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02087 | SCR_001253 | SciCrunch Registry | 2026-10-31 12:12:48 | 0 | ||||||||
|
CNVtools Resource Report Resource Website 10+ mentions |
CNVtools (RRID:SCR_001250) | CNVtools | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies. | genetic variability, copy number variant, genetic association |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18776912 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02090 | SCR_001250 | SciCrunch Registry | CNVtools - A package to test genetic association with CNV data | 2026-10-31 12:12:48 | 12 | ||||||
|
CGEN Resource Report Resource Website 10+ mentions |
CGEN (RRID:SCR_001251) | CGEN | data analysis software, data processing software, software application, software resource | Software R package for analysis of case-control studies in genetic epidemiology. | genetic, epidemiology, r, case-control, clustering, multiple comparison, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21387464 | Free, Available for download, Freely available | OMICS_02089 | SCR_001251 | SciCrunch Registry | CGEN - An R package for analysis of case-control studies in genetic epidemiology | 2026-10-31 12:12:48 | 18 | ||||||
|
multtest Resource Report Resource Website 10+ mentions |
multtest (RRID:SCR_001255) | multtest | software resource | Software package for non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. | differential expression, microarray, multiple comparison, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:multtest, OMICS_02085 | https://bio.tools/multtest | SCR_001255 | SciCrunch Registry | multtest - Resampling-based multiple hypothesis testing | 2026-10-31 12:12:48 | 37 |
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