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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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methVisual Resource Report Resource Website 1+ mentions |
methVisual (RRID:SCR_006705) | methVisual | software resource | Software package that allows the visualization of DNA methylation data after bisulfite sequencing. |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00604 | SCR_006705 | methVisual - Methods for visualization and statistics on DNA methylation data | 2026-08-01 12:03:18 | 1 | ||||||||
|
seqbias Resource Report Resource Website 10+ mentions |
seqbias (RRID:SCR_006832) | seqbias | software resource | Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_01237, biotools:seqbias, BioTools:seqbias | https://bio.tools/seqbias, https://bio.tools/seqbias, https://bio.tools/seqbias | SCR_006832 | seqbias - Estimation of per-position bias in high-throughput sequencing data | 2026-08-01 12:03:13 | 30 | ||||||
|
arrayMagic Resource Report Resource Website 1+ mentions |
arrayMagic (RRID:SCR_010933) | arrayMagic | software resource | Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data |
is listed by: OMICtools has parent organization: Bioconductor |
BSD License | OMICS_00743 | SCR_010933 | arrayMagic - two-colour cDNA array quality control and preprocessing | 2026-08-01 12:04:18 | 1 | ||||||||
|
CGHnormaliter Resource Report Resource Website 1+ mentions |
CGHnormaliter (RRID:SCR_002936) | software resource | Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). | standalone software, mac os x, unix/linux, windows, r, array comparative genomic hybridization, copy number alteration, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20418341 | Free, Available for download, Freely available | OMICS_02572 | http://www.bioconductor.org/packages/release/bioc/html/CGHnormaliter.html | SCR_002936 | CGHnormaliter - Normalization of array CGH data with imbalanced aberrations. | 2026-08-01 12:02:15 | 2 | ||||||
|
Chimera Resource Report Resource Website 100+ mentions |
Chimera (RRID:SCR_002959) | software resource | A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. | software package, unix/linux, mac os x, windows, r, infrastructure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
PMID:25286921 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_06335 | SCR_002959 | chimera - A package for secondary analysis of fusion products | 2026-08-01 12:01:59 | 377 | |||||||
|
Triplex Resource Report Resource Website 10+ mentions |
Triplex (RRID:SCR_003061) | software resource | Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. | software package, mac os x, unix/linux, windows, r, gene regulation, sequence matching, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23709494 | Free, Available for download, Freely available | OMICS_06259, biotools:triplex | http://www.fi.muni.cz/~lexa/triplex/, https://bio.tools/triplex | SCR_003061 | triplex - Search and visualize intramolecular triplex-forming sequences in DNA | 2026-08-01 12:02:25 | 10 | ||||||
|
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 | 2026-08-01 12:01:40 | 3 | |||||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, 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:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-08-01 12:01:24 | 1 | ||||||
|
ARRmNormalization Resource Report Resource Website |
ARRmNormalization (RRID:SCR_001292) | ARRmNormalization | software resource | Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay. | dna methylation, microarray, preprocessing, two channel, illumina |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02044 | SCR_001292 | ARRmNormalization - Adaptive Robust Regression normalization for Illumina methylation data | 2026-08-01 12:01:27 | 0 | |||||||
|
methylMnM Resource Report Resource Website 1+ mentions |
methylMnM (RRID:SCR_001289) | methylMnM | software resource | Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison. | dna methylation, sequencing, medip-seq, mre-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v3 | OMICS_02047 | SCR_001289 | methylMnM - detect different methylation level (DMR) | 2026-08-01 12:01:27 | 9 | |||||||
|
MergeMaid Resource Report Resource Website 1+ mentions |
MergeMaid (RRID:SCR_001221) | MergeMaid | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival. | differential expression, microarray, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16646808 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02124 | SCR_001221 | Merge Maid | 2026-08-01 12:01:35 | 3 | ||||||
|
iterativeBMAsurv Resource Report Resource Website |
iterativeBMAsurv (RRID:SCR_001254) | iterativeBMAsurv | software resource | Software package providing a variable selection method for applying survival analysis to microarray data. | microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19245714 | GNU General Public License, v2 or newer | OMICS_02086 | SCR_001254 | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis, iterativeBMAsurv - The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis | 2026-08-01 12:01:26 | 0 | ||||||
|
snpStats: SnpMatrix and XSnpMatrix classes and methods Resource Report Resource Website 50+ mentions |
snpStats: SnpMatrix and XSnpMatrix classes and methods (RRID:SCR_001249) | snpStats | software resource | Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies. | r, single nucleotide polymorphism, genetic variability, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:16720584 | Free, Available for download, Freely available | OMICS_02091 | SCR_001249 | 2026-08-01 12:01:44 | 78 | |||||||
|
exomeCopy Resource Report Resource Website 10+ mentions |
exomeCopy (RRID:SCR_001276) | exomeCopy | software resource | Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count. | copy number variation, genetics, sequencing, exome |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23089826 | Free, Available for download, Freely available | OMICS_02062 | http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html | SCR_001276 | exomeCopy - Copy number variant detection from exome sequencing read depth | 2026-08-01 12:01:26 | 15 | |||||
|
SMAP Resource Report Resource Website 100+ mentions |
SMAP (RRID:SCR_001270) | SMAP | software resource | Software package providing functions and classes for DNA copy number profiling of array-CGH data. | copy number variation, microarray, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18204059 | Free, Available for download, Freely available | OMICS_02068 | SCR_001270 | SMAP - A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling | 2026-08-01 12:01:26 | 199 | ||||||
|
wateRmelon Resource Report Resource Website 100+ mentions |
wateRmelon (RRID:SCR_001296) | wateRmelon | software resource | Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages. | dna methylation, microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23631413 | Free, Available for download, Freely available | OMICS_02039, biotools:watermelon | https://bio.tools/watermelon | SCR_001296 | 2026-08-01 12:01:46 | 296 | ||||||
|
oneChannelGUI Resource Report Resource Website 10+ mentions |
oneChannelGUI (RRID:SCR_001325) | oneChannelGUI | software resource | Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, rna-seq, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:17875544 | Free, Available for download, Freely available | biotools:onechannelgu, OMICS_02004 | http://www.bioconductor.org/packages/release/bioc/html/oneChannelGUI.html | SCR_001325 | 2026-08-01 12:01:27 | 13 | ||||||
|
CYCLE Resource Report Resource Website 10+ mentions |
CYCLE (RRID:SCR_001328) | CYCLE | software resource | Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models. | r, microarray, time course, periodic expression pattern, time-series, 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:18310054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02010, biotools:cycle | http://www.bioconductor.org/packages/release/bioc/html/cycle.html, https://bio.tools/cycle | SCR_001328 | 2026-08-01 12:01:28 | 31 | ||||||
|
LMGene Resource Report Resource Website 1+ mentions |
LMGene (RRID:SCR_001329) | LMGene | software resource | Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays. | differential expression, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02009 | http://www.bioconductor.org/packages/release/bioc/html/LMGene.html | SCR_001329 | 2026-08-01 12:01:48 | 4 | |||||||
|
affylmGUI Resource Report Resource Website 10+ mentions |
affylmGUI (RRID:SCR_001320) | affylmGUI | software resource | R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11. | affymetrix, differential expression, r, data import, differential expression, gui, microarray, multiple comparison, one channel, preprocessing, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia has parent organization: Bioconductor |
PMID:16455752 | Free, Available for download, Freely available | biotools:affylmgui, OMICS_02016 | http://www.bioconductor.org/packages/release/bioc/html/affylmGUI.html, https://bio.tools/affylmgui | SCR_001320 | Affymetrix linear modeling Graphical User Interface | 2026-08-01 12:01:47 | 31 |
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