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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RchyOptimyx Resource Report Resource Website 1+ mentions |
RchyOptimyx (RRID:SCR_001889) | software resource | Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response). | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23044634 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05637 | SCR_001889 | RchyOptimyx - Optimyzed Cellular Hierarchies for Flow Cytometry, RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry | 2026-09-05 06:24:41 | 3 | |||||||
|
SPADE Resource Report Resource Website 100+ mentions |
SPADE (RRID:SCR_001810) | data analysis software, data processing software, data visualization software, software application, software resource | An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gui, graph, network, visualization |
is listed by: OMICtools has parent organization: Bioconductor is a plug in for: FlowJo |
PMID:21964415 | Free, Available for download, Freely available | OMICS_05639 | http://cytospade.org/ | http://www.bioconductor.org/packages/release/bioc/html/spade.html | SCR_001810 | Spanning tree Progression of Density normalized Events, SPADE - An analysis and visualization tool for Flow Cytometry | 2026-09-05 06:24:39 | 285 | |||||
|
flowType Resource Report Resource Website 1+ mentions |
flowType (RRID:SCR_001957) | software resource | Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22383736 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05613 | SCR_001957 | flowType - Phenotyping Flow Cytometry Assays | 2026-09-05 06:24:42 | 9 | |||||||
|
ADaCGH2 Resource Report Resource Website |
ADaCGH2 (RRID:SCR_001981) | software resource | Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data. | standalone software, mac os x, unix/linux, windows, r, copy number variant, microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24532724 | Free, Available for download, Freely available | biotools:adacgh2, OMICS_03697 | https://bio.tools/adacgh2 | SCR_001981 | ADaCGH2 - Analysis of big data from aCGH experiments using parallel computing and ff objects | 2026-09-05 06:24:42 | 0 | ||||||
|
PurBayes Resource Report Resource Website 10+ mentions |
PurBayes (RRID:SCR_002068) | software resource | An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data. | 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:23749958 | Free, Available for download, Freely available | biotools:purbayes, OMICS_03561 | https://bio.tools/purbayes | http://cran.r-project.org/web/packages/PurBayes/ | SCR_002068 | PurBayes: Bayesian Estimation of Tumor Purity and Clonality | 2026-09-05 06:24:43 | 11 | |||||
|
Vennt Resource Report Resource Website 1+ mentions |
Vennt (RRID:SCR_002083) | software resource | A web-tool to generate dynamic Venn diagrams for differential gene expression. | unix/linux, mac os x, windows, python | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_03549 | https://github.com/drpowell/vennt | SCR_002083 | Vennt - Dynamic Venn diagrams for Differential Gene Expression | 2026-09-05 06:24:43 | 7 | |||||||
|
TEQC Resource Report Resource Website 10+ mentions |
TEQC (RRID:SCR_001943) | software resource | An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on. | standalone software, unix/linux, mac os x, windows, r, genetics, microarray, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21398674 | Free, Available for download, Freely available | OMICS_03602 | SCR_001943 | TEQC - Quality control for target capture experiments | 2026-09-05 06:24:42 | 14 | |||||||
|
flowViz Resource Report Resource Website 10+ mentions |
flowViz (RRID:SCR_002075) | software resource | Software that provides visualization tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18245128 | Free, Available for download, Freely available | OMICS_05615 | SCR_002075 | flowViz - Visualization for flow cytometry | 2026-09-05 06:24:43 | 31 | |||||||
|
PRADA Resource Report Resource Website 50+ mentions |
PRADA (RRID:SCR_011906) | PRADA | software resource | A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01408, biotools:prada-rnaseq | https://bio.tools/prada-rnaseq | SCR_011906 | Pipeline for RNA-Sequencing Data Analysis | 2026-09-05 06:27:15 | 51 | |||||||
|
miRPlant Resource Report Resource Website 10+ mentions |
miRPlant (RRID:SCR_012105) | software resource | A user-friendly plant miRNA prediction tool. | applet, unix/linux, mac os x, windows, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25117656 | GNU General Public License | OMICS_05325, biotools:mirplant | https://bio.tools/mirplant | SCR_012105 | 2026-09-05 06:27:20 | 14 | |||||||
|
ChiBE Resource Report Resource Website 1+ mentions |
ChiBE (RRID:SCR_012110) | software resource | An editing and visualization software tool for pathway models represented by the BioPAX format, using SBGN Process Description Language, based on Chisio. | mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:25086704 | Free, Public | OMICS_05454 | SCR_012110 | Chisio BioPAX Editor | 2026-09-05 06:27:20 | 3 | |||||||
|
diCal-IBD Resource Report Resource Website |
diCal-IBD (RRID:SCR_012111) | software resource | Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. | standalone software, unix/linux, mac os x, windows, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25147361 | BSD License | OMICS_05459 | SCR_012111 | 2026-09-05 06:27:20 | 0 | ||||||||
|
SketchEl Resource Report Resource Website |
SketchEl (RRID:SCR_012082) | software resource | An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. | applet, mac os x, unix/linux, windows, java, javascript |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04982 | SCR_012082 | 2026-09-05 06:27:20 | 0 | |||||||||
|
MCDL Resource Report Resource Website 1+ mentions |
MCDL (RRID:SCR_012084) | software resource | A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. | applet, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05001 | SCR_012084 | 2026-09-05 06:27:20 | 2 | ||||||||||
|
SearchGUI Resource Report Resource Website 100+ mentions |
SearchGUI (RRID:SCR_012054) | software resource | Software providing a user-friendly, lightweight and open-source graphical user interface for configuring and running the freely available OMSSA and X!Tandem search engines simultaneously. | mac os x, unix/linux, windows |
is listed by: OMICtools has parent organization: Google Code |
PMID:21337703 | Apache License | OMICS_03352 | SCR_012054 | 2026-09-05 06:27:19 | 157 | ||||||||
|
COBRApy Resource Report Resource Website 100+ mentions |
COBRApy (RRID:SCR_012096) | software resource | Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods. | software package, mac os x, unix/linux, windows, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23927696 DOI:10.1186/1752-0509-7-74 |
OMICS_05190, biotools:cobrapy | https://bio.tools/cobrapy | https://sources.debian.org/src/python3-cobra/ | SCR_012096 | COBRA for Python | 2026-09-05 06:27:20 | 341 | ||||||
|
jmzTab Resource Report Resource Website 1+ mentions |
jmzTab (RRID:SCR_003481) | software resource | A Java interface to the mzTab data exchange format for reporting a summary of proteomics results. | standalone software, mac os x, unix/linux, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24659499 | Apache License, v2 | OMICS_04542, biotools:jmztab | https://bio.tools/jmztab | SCR_003481 | 2026-09-05 06:25:04 | 1 | |||||||
|
Polyester Resource Report Resource Website 100+ mentions |
Polyester (RRID:SCR_003602) | data analysis software, data processing software, simulation software, software application, software resource | An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code | standalone software, unix/linux, mac os x, windows, r, rna-seq | is listed by: OMICtools | OMICS_04272 | SCR_003602 | 2026-09-05 06:25:06 | 491 | ||||||||||
|
DMRforPairs Resource Report Resource Website 1+ mentions |
DMRforPairs (RRID:SCR_005702) | software resource | Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. | standalone software, mac os x, unix/linux, windows, r, annotation, dna methylation, differential methylation, microarray, report writing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24884391 | GNU General Public License, v2 or greater | biotools:dmrforpairs, OMICS_04059 | https://bio.tools/dmrforpairs | SCR_005702 | DMR2+, DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles | 2026-09-05 06:25:40 | 4 | ||||||
|
Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden, https://sources.debian.org/src/staden/ | SCR_005629 | Staden Package | 2026-09-05 06:25:39 | 87 |
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