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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | SciCrunch Registry | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-10-31 12:13:16 | 4 | ||||||
|
BRAIN Resource Report Resource Website 10+ mentions |
BRAIN (RRID:SCR_003018) | software resource | Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23350948 | GNU General Public License, v2 | biotools:brain, OMICS_02410 | https://bio.tools/brain | SCR_003018 | SciCrunch Registry | Baffling Recursive Algorithm for Isotopic distributioN calculations, Baffling Recursive Algorithm for Isotope distributioN | 2026-10-31 12:13:17 | 47 | ||||||
|
SurvComp Resource Report Resource Website 50+ mentions |
SurvComp (RRID:SCR_003054) | survcomp | software resource | R package providing functions to assess and to compare the performance of risk prediction (survival) models. | differential expression, gene expression, visualization, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21903630 | Free, Available for download, Freely available | OMICS_02373 | SCR_003054 | SciCrunch Registry | survcomp - Performance Assessment and Comparison for Survival Analysis | 2026-10-31 12:13:17 | 61 | ||||||
|
Piano Resource Report Resource Website 100+ mentions |
Piano (RRID:SCR_003200) | data analysis software, data processing software, software application, software resource | Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses. | r, omics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chalmers University of Technology; Gothenburg; Sweden has parent organization: Bioconductor |
PMID:23444143 | Free, Available for download, Freely available | OMICS_01558, biotools:piano | https://bio.tools/piano | SCR_003200 | SciCrunch Registry | 2026-10-31 12:13:20 | 188 | |||||||
|
ddCt Resource Report Resource Website 100+ mentions |
ddCt (RRID:SCR_003396) | ddCt | software resource | Software package providing an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. It requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions. | differential expression, gene expression, microtitre plate assay, q-pcr |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02312 | SCR_003396 | SciCrunch Registry | Delta-Delta-Ct | 2026-10-31 12:13:24 | 328 | |||||||
|
ggbio Resource Report Resource Website 10+ mentions |
ggbio (RRID:SCR_003313) | software resource | An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. | standalone software, unix/linux, mac os x, windows, r, infrastructure, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22937822 | Free, Available for download, Freely available | biotools:ggbio, OMICS_04660 | http://www.tengfei.name/ggbio/, https://bio.tools/ggbio | SCR_003313 | SciCrunch Registry | ggbio - Visualization tools for genomic data | 2026-10-31 12:13:23 | 16 | ||||||
|
OmicCircos Resource Report Resource Website 50+ mentions |
OmicCircos (RRID:SCR_003292) | software resource | An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. | standalone software, unix/linux, mac os x, windows, r, annotation, statistical method, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24526832 | Free, Available for download, Freely available | OMICS_04659 | http://www.bioconductor.org/packages/release/bioc/html/OmicCircos.html | SCR_003292 | SciCrunch Registry | OmicCircos: High-quality circular visualization of omic data | 2026-10-31 12:13:21 | 83 | ||||||
|
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 | ||||||
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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 | ||||||
|
ITALICS Resource Report Resource Website |
ITALICS (RRID:SCR_001274) | ITALICS | software resource | Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set. | affymetrix, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18252739 | Free, Available for download, Freely available | OMICS_02064 | SCR_001274 | SciCrunch Registry | 2026-10-31 12:12:48 | 0 | |||||||
|
GenoSet Resource Report Resource Website |
GenoSet (RRID:SCR_001275) | GenoSet | data analysis software, data processing software, software application, software resource | Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. | copy number variation, data representation, infrastructure, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License, v2 | OMICS_02063 | SCR_001275 | SciCrunch Registry | genoset - Provides classes similar to ExpressionSet for copy number analysis | 2026-10-31 12:12:48 | 0 |
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