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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-12 12:55:38 | 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 | 2026-09-12 12:55:37 | 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 | 2026-09-12 12:55:40 | 130 | |||||||
|
r3Cseq Resource Report Resource Website 10+ mentions |
r3Cseq (RRID:SCR_003198) | r3Cseq | data analysis software, data processing software, software application, software resource | An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results. | next-generation sequencing, genomic, interaction, chromosome conformation capture, chromosome, 3c-seq, r |
is listed by: OMICtools has parent organization: University of Bergen; Bergen; Norway has parent organization: Bioconductor |
PMID:23671339 | Free, Freely available | OMICS_01560 | SCR_003198 | 2026-09-12 12:55:53 | 24 | |||||||
|
QDNAseq Resource Report Resource Website 100+ mentions |
QDNAseq (RRID:SCR_003174) | software resource | Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively. | software package, unix/linux, mac os x, windows, r, copy number variation, dna-seq, genetics, genome annotation, preprocessing, quality control, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25236618 | Free, Available for download, Freely available | OMICS_05902, biotools:qdnaseq | https://github.com/ccagc/QDNAseq, https://bio.tools/qdnaseq | SCR_003174 | QDNAseq - Quantitative DNA sequencing for chromosomal aberrations | 2026-09-12 12:55:53 | 168 | ||||||
|
LaSSO Resource Report Resource Website 100+ mentions |
LaSSO (RRID:SCR_003418) | software resource | An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns. | standalone software, r, FASEB list | is listed by: OMICtools | PMID:24709818 | Free, Available for download, Freely available | OMICS_04622 | SCR_003418 | Lariat Sequence Site Origin | 2026-09-12 12:55:57 | 224 | |||||||
|
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 | ||||||
|
g:Profiler Resource Report Resource Website 1000+ mentions |
g:Profiler (RRID:SCR_006809) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for functional enrichment analysis and conversions of gene lists. Web based tool for functional profiling of gene lists from large scale experiments. Has web interface with powerful visualization. Used for analyzing data from any organism. | gene, high-throughput, genomics, visualization, statistical analysis, slimmer-type tool, term enrichment, protein interaction, functional similarity, analysis, coexpression, gene id, network enrichment analysis, orthology mapping, genomic locus, ontology or annotation visualization, other analysis, ortholog, functional profile, gene list, ontology, pathway, transcription factor, microrna, regulatory motif, protein-protein interaction, biomolecule, gene expression, gene, homology, single nucleotide polymorphism, dna polymorphism, chromosome, network analysis, disease gene, r |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Ensembl is related to: Ensembl Genomes has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group works with: gProfiler2 |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:21646343 PMID:17478515 PMID:31066453 |
Free, Freely available | OMICS_02223, nif-0000-31975 | SCR_006809 | G:Profiler, g:profiler, gProfiler | 2026-09-12 12:56:46 | 2310 | ||||||
|
BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-09-12 12:57:11 | 39 | ||||||
|
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 | |||||||
|
Cascade Resource Report Resource Website 50+ mentions |
Cascade (RRID:SCR_005861) | Cascade | software resource | R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, windows, gene expression, perturbation, network, diffusion, signal, temporal gene network, gene regulatory network, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Strasbourg; Strasbourg; France |
PMID:24307703 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02249, biotools:cascade | http://www-math.u-strasbg.fr/genpred/spip.php?rubrique4, https://bio.tools/cascade | SCR_005861 | 2026-09-12 12:56:32 | 92 | ||||||
|
IQRray Resource Report Resource Website 1+ mentions |
IQRray (RRID:SCR_006057) | IQRray | software resource | Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments. | r, affymetrix, microarray, quality control, evolutionary conservation, expression profile, probe |
is listed by: OMICtools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:24451627 | Free, Public | OMICS_02244 | SCR_006057 | 2026-09-12 12:56:34 | 2 | |||||||
|
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 | |||||||
|
CAFE Resource Report Resource Website 500+ mentions |
CAFE (RRID:SCR_005983) | CAFE | software resource | R software package for the detection of gross chromosomal abnormalities from gene expression microarray data. | affymetrix, r, chromosomal abnormality, gene expression, microarray, chromosome, linux, windows |
is listed by: OMICtools has parent organization: Bitbucket |
PMID:24451624 | GNU General Public License, v3, Acknowledgement requested | OMICS_02245 | SCR_005983 | 2026-09-12 12:56:34 | 883 | |||||||
|
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 | |||||||
|
AbsCN-seq Resource Report Resource Website 1+ mentions |
AbsCN-seq (RRID:SCR_006409) | AbsCN-seq | software resource | Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data. | r, statistics, purity, ploidy, absolute copy number, next-generation sequencing |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
Tumor, Cancer | PMID:24389661 | Free, Public | OMICS_02202 | SCR_006409 | 2026-09-12 12:56:39 | 7 | ||||||
|
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 | 2026-09-12 12:55:41 | 4 | |||||
|
Iterative Signature Algorithm Resource Report Resource Website |
Iterative Signature Algorithm (RRID:SCR_002327) | isa2, ISA | software resource | A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix. | standalone software, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:12689096 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:isa, OMICS_03487 | https://bio.tools/isa | SCR_002327 | isa2: The Iterative Signature Algorithm | 2026-09-12 12:55:39 | 0 | |||||
|
ExomeDepth Resource Report Resource Website 100+ mentions |
ExomeDepth (RRID:SCR_002663) | software resource | Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | software package, unix/linux, mac os x, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:22942019 | Free, Available for download, Freely available | OMICS_05443, biotools:exomedepth | https://bio.tools/exomedepth | SCR_002663 | 2026-09-12 12:55:44 | 295 | |||||||
|
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 | 2026-09-12 12:55:44 | 68 |
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