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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-19 12:50:14 | 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 | 2026-09-19 12:50:13 | 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 | 2026-09-19 12:50:19 | 224 | |||||||
|
flowMap Resource Report Resource Website 1+ mentions |
flowMap (RRID:SCR_002269) | software resource | Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process. | software package, mac os x, unix/linux, windows, r, flow cytometry, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_05600 | SCR_002269 | flowMap - A probabilistic algorithm for matching and comparing multiple flow cytometry samples | 2026-09-19 12:49:55 | 5 | ||||||||
|
shinyTANDEM Resource Report Resource Website |
shinyTANDEM (RRID:SCR_002169) | software resource | Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files. | mac os x, unix/linux, windows, r, mass spectrometry, proteomics |
uses: rTANDEM is listed by: OMICtools has parent organization: Bioconductor |
PMID:24700319 | Free, Available for download, Freely available | OMICS_03517 | http://www.bioconductor.org/packages/release/bioc/html/shinyTANDEM.html | http://www.bioconductor.org/packages/devel/bioc/html/shinyTANDEM.html, Resource:rTANDEM | SCR_002169 | 2026-09-19 12:49:54 | 0 | ||||||
|
flowMatch Resource Report Resource Website 1+ mentions |
flowMatch (RRID:SCR_002283) | software resource | Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22536861 | Free, Available for download, Freely available | OMICS_05602 | SCR_002283 | flowMatch - Matching and meta-clustering in flow cytometry | 2026-09-19 12:49:56 | 1 | |||||||
|
flowMeans Resource Report Resource Website 1+ mentions |
flowMeans (RRID:SCR_002275) | software resource | Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor is a plug in for: FlowJo |
PMID:21182178 | Artistic License, v2 | OMICS_05603 | SCR_002275 | flowMeans: Non-parametric Flow Cytometry Data Gating, flowMeans - Non-parametric Flow Cytometry Data Gating | 2026-09-19 12:49:55 | 7 | |||||||
|
RankAggreg Resource Report Resource Website 10+ mentions |
RankAggreg (RRID:SCR_002225) | software resource | Software package that performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:19228411 | GNU Lesser General Public License, v2, v2.1, v3 | OMICS_03526 | SCR_002225 | RankAggreg: Weighted rank aggregation | 2026-09-19 12:49:55 | 48 | |||||||
|
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 | 2026-09-19 12:49:55 | 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 | 2026-09-19 12:49:56 | 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 | 2026-09-19 12:49:58 | 130 | |||||||
|
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 | 2026-09-19 12:49:59 | 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 | 2026-09-19 12:49:57 | 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 | 2026-09-19 12:50:05 | 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 | 2026-09-19 12:50:02 | 68 | ||||||
|
R-package for adaptive DWI analysis Resource Report Resource Website |
R-package for adaptive DWI analysis (RRID:SCR_002528) | R-package for adaptive DWI analysis | data processing software, image processing software, software application, software resource | The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, diffusion weighted, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155934 | SCR_002528 | 2026-09-19 12:50:00 | 0 | ||||||||
|
FisHiCal Resource Report Resource Website |
FisHiCal (RRID:SCR_002799) | software resource | Software that integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis. | standalone software, software package, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:25061071 | Free, Freely available, Available for download | OMICS_05207 | SCR_002799 | FisHiCal: Iterative FISH-based Calibration of Hi-C Data | 2026-09-19 12:50:05 | 0 | |||||||
|
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 | 2026-09-19 12:50:08 | 3 | ||||||
|
MetaDE Resource Report Resource Website 1+ mentions |
MetaDE (RRID:SCR_000199) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:22863766 | Free, Available for download, Freely available | OMICS_04033 | http://cran.r-project.org/web/packages/MetaDE/ | SCR_000199 | MetaDE: Microarray meta-analysis for differentially expressed gene detection | 2026-09-19 12:49:17 | 1 | ||||||
|
flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-09-19 12:49:22 | 21 |
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