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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PyroHMMvar Resource Report Resource Website 1+ mentions |
PyroHMMvar (RRID:SCR_002073) | PyroHMMvar | software resource | A software program to call short indels and SNPs for Ion Torrent and 454 data. |
is listed by: OMICtools has parent organization: Google Code |
PMID:23995392 | Free, Available for download, Freely available | OMICS_00069 | https://code.google.com/p/pyrohmmvar/ | SCR_002073 | 2026-08-01 12:01:58 | 1 | |||||||
|
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 | 2026-08-01 12:02:09 | 5 | ||||||||
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | 2026-08-01 12:01:42 | 11 | |||||||
|
Matchprot Resource Report Resource Website |
Matchprot (RRID:SCR_002163) | software resource | A pairwise protein structure alignment software. | standalone software, c |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17338826 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03666 | SCR_002163 | 2026-08-01 12:02:00 | 0 | ||||||||
|
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 | 2026-08-01 12:02:08 | 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 | 2026-08-01 12:02:03 | 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 | 2026-08-01 12:02:09 | 6 | |||||||
|
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 | 2026-08-01 12:02:01 | 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 | 2026-08-01 12:02:08 | 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 | 2026-08-01 12:01:43 | 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 | 2026-08-01 12:01:47 | 126 | |||||||
|
SBARS Resource Report Resource Website |
SBARS (RRID:SCR_002371) | software resource | Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes. | linux, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24532721 | OMICS_03432, biotools:sbars | https://bio.tools/sbars | SCR_002371 | S.B.A.R.S, S.B.A.R.S., S.B.A.R.S - Spectral-Based Approach for Repeats Search, Spectral-Based Approach for Repeats Search | 2026-08-01 12:02:05 | 0 | |||||||
|
DOSY Toolbox Resource Report Resource Website |
DOSY Toolbox (RRID:SCR_002409) | software resource | Software toolbox for processing PFG NMR diffusion data that aims to incorporate many of the important processing schemes. It has a graphical user interface to make it easy to access a variety of different processing schemes (and a command mode for more advanced options). It is written in MATLAB, but can also be obtained as free standing compiled version that does not require a MATLAB installation. The MATLAB version runs on any platform, and the compiled version is presently available for Windows, Linux, and Mac. | diffusion-ordered spectroscopy, matlab, mac os x, unix/linux, windows |
is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
PMID:19666235 | Free, Available for download, Freely available | OMICS_03393 | SCR_002409 | The DOSY Toolbox processing PFG-NMR diffusion data, The DOSY Toolbox | 2026-08-01 12:02:06 | 0 | |||||||
|
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 | 2026-08-01 12:02:10 | 4 | |||||
|
PolyPhred Resource Report Resource Website 100+ mentions |
PolyPhred (RRID:SCR_002337) | PolyPhred | software resource | Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool. | windows, sequence, nucleotide substitution, heterozygote, polymorphic, genotype, single nucleotide polymorphism, fluorescence, single nucleotide substitution, polymorphism, insertion, deletion, indel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:17115056 PMID:16493422 PMID:9207020 |
Free for academic use, Commercial use requires a license | biotools:polyphred, OMICS_01815 | https://bio.tools/polyphred | SCR_002337 | 2026-08-01 12:01:46 | 123 | ||||||
|
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 | 2026-08-01 12:02:09 | 0 | |||||
|
HaploClique Resource Report Resource Website 1+ mentions |
HaploClique (RRID:SCR_002353) | software resource | Software providing a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples. | standalone software | is listed by: OMICtools | PMID:24675810 | OMICS_03442 | SCR_002353 | 2026-08-01 12:01:46 | 5 | |||||||||
|
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 | 2026-08-01 12:01:52 | 65 | ||||||
|
JATAC Resource Report Resource Website |
JATAC (RRID:SCR_003978) | JATAC | software resource | Software program for filtering duplicate 454 sequences by comparing flowgram information. | is listed by: OMICtools | PMID:23376350 | OMICS_01055 | SCR_003978 | 2026-08-01 12:02:26 | 0 | |||||||||
|
Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | Quantitative Enrichment of Sequence Tags: QuEST | 2026-08-01 12:02:37 | 49 |
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