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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
flowPlots Resource Report Resource Website |
flowPlots (RRID:SCR_002177) | software resource | Software for analysis plots and data class for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, data representation, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05608 | SCR_002177 | flowPlots: analysis plots and data class for gated flow cytometry data | 2026-09-05 06:24:44 | 0 | ||||||||
|
metaRNASeq Resource Report Resource Website 10+ mentions |
metaRNASeq (RRID:SCR_002174) | software resource | Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: SMAGEXP has parent organization: CRAN |
PMID:24678608 | Free, Available for download, Freely available | OMICS_03527 | SCR_002174 | metaRNASeq: Meta-analysis of RNA-seq data | 2026-09-05 06:24:44 | 35 | |||||||
|
DEMI Resource Report Resource Website 1+ mentions |
DEMI (RRID:SCR_002291) | software resource | R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes. | standalone software, affymetrix, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24586062 | Free, Available for download, Freely available, Acknowledgement requested | OMICS_03438 | http://cran.r-project.org/web/packages/demi/ | SCR_002291 | demi: Differential Expression from Multiple Indicators, Differential Expression from Multiple Indicators | 2026-09-05 06:24:46 | 6 | ||||||
|
flowCore Resource Report Resource Website 100+ mentions |
flowCore (RRID:SCR_002205) | software resource | A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is used by: flowBeads is listed by: OMICtools has parent organization: Bioconductor |
PMID:19358741 | Artistic License, v2 | OMICS_05596 | SCR_002205 | flowCore: Basic structures for flow cytometry data | 2026-09-05 06:24:45 | 376 | |||||||
|
flowBeads Resource Report Resource Website |
flowBeads (RRID:SCR_002440) | software resource | Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
uses: flowCore is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available | OMICS_05592 | SCR_002440 | flowBeads: Analysis of flow bead data | 2026-09-05 06:24:48 | 0 | ||||||||
|
flowCyBar Resource Report Resource Website 1+ mentions |
flowCyBar (RRID:SCR_002319) | software resource | A software package to analyze flow cytometric data using gate information to follow population / community dynamics. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_05597 | SCR_002319 | flowCyBar - Analyze flow cytometric data using gate information | 2026-09-05 06:24:46 | 7 | ||||||||
|
MBASED Resource Report Resource Website 10+ mentions |
MBASED (RRID:SCR_002584) | software resource | Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection. | software package, unix/linux, mac os x, windows, r, gene expression, sequencing, transcription |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25315065 | Free, Available for download, Freely available | OMICS_05502 | http://www.bioconductor.org/packages/release/bioc/html/MBASED.html | SCR_002584 | Meta-analysis Based Allele-Specific Expression Detection, MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection | 2026-09-05 06:24:50 | 17 | ||||||
|
JChemPaint Resource Report Resource Website 1+ mentions |
JChemPaint (RRID:SCR_000095) | JCP | software resource | Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK). | applet, mac os x, unix/linux, windows, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_04959 | https://github.com/JChemPaint/jchempaint | SCR_000095 | 2026-09-05 06:24:11 | 1 | |||||||
|
flowCL Resource Report Resource Website |
flowCL (RRID:SCR_000046) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
has parent organization: Bioconductor has parent organization: BC Cancer Agency |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05594 | SCR_000046 | flowCL - Semantic labelling of flow cytometric cell populations | 2026-09-05 06:24:09 | 0 | ||||||||
|
Cbrowse Resource Report Resource Website |
Cbrowse (RRID:SCR_000044) | software resource | Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. | unix/linux, mac os x, windows |
has parent organization: Google Code has parent organization: Miami University; Ohio; USA |
PMID:22789590 | Free, Available for download, Freely available | OMICS_04048 | SCR_000044 | 2026-09-05 06:24:10 | 0 | ||||||||
|
RmiR.Hs.miRNA Resource Report Resource Website |
RmiR.Hs.miRNA (RRID:SCR_000101) | software resource | Software package for various databases of microRNA Targets. | software package, unix/linux, mac os x, windows, r, annotation data, custom db schema, mirna |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05797 | SCR_000101 | RmiR.Hs.miRNA: Various databases of microRNA Targets | 2026-09-05 06:24:12 | 0 | ||||||||
|
FACS Resource Report Resource Website 1+ mentions |
FACS (RRID:SCR_000055) | FACS | software resource | Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence. | unix/linux, sequence, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SciLifeLab |
PMID:20472541 | Free, Available for download, Freely available | OMICS_02147, biotools:facs | https://bio.tools/facs | SCR_000055 | Fast and Accurate Classification of Sequences | 2026-09-05 06:24:11 | 6 | |||||
|
A5-miseq Resource Report Resource Website 100+ mentions |
A5-miseq (RRID:SCR_012148) | software resource | Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming. | standalone software, illumina, unix/linux, mac os x, bio.tools |
is used by: Nephele is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25338718 | GNU General Public License | OMICS_06339, biotools:a5-miseq | https://bio.tools/a5-miseq | SCR_012148 | 2026-09-05 06:27:21 | 202 | |||||||
|
PLEK Resource Report Resource Website 100+ mentions |
PLEK (RRID:SCR_012132) | software resource | An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data. | standalone software, roche, pacific biosciences, unix/linux, c, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25239089 | GNU General Public License | biotools:plek, OMICS_05839 | https://bio.tools/plek | SCR_012132 | PLEK: predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme | 2026-09-05 06:27:21 | 134 | ||||||
|
LifeScope Resource Report Resource Website 100+ mentions |
LifeScope (RRID:SCR_013234) | LifeScope | software resource | Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC). | unix/linux, life technologies, linux, next-generation sequencing | has parent organization: Life Technologies | Acknowledgement requested | OMICS_00667 | SCR_013234 | LifeScope Genomic Analysis Software | 2026-09-05 06:27:34 | 200 | |||||||
|
metaMA Resource Report Resource Website |
metaMA (RRID:SCR_000408) | software resource, software toolkit | Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: CRAN is related to: SMAGEXP |
Scottish Government Rural and Environment Research and Analysis Directorate | PMID:19628502 | Free, Available for download, Freely available | OMICS_03524 | SCR_000408 | Meta-analysis for MicroArrays, Meta analysis for MicroArrays | 2026-09-05 06:32:21 | 0 | ||||||
|
VennDiagram Resource Report Resource Website 1000+ mentions |
VennDiagram (RRID:SCR_002414) | software resource, software toolkit | Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. | Venn and Euler plots, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: Debian is related to: jVenn has parent organization: CRAN |
PMID:21269502 | Free, Available for download, Freely available | OMICS_05570 | https://sources.debian.org/src/r-cran-venndiagram/ | SCR_002414 | VennDiagram: Generate high-resolution Venn and Euler plots | 2026-09-05 06:32:26 | 2138 | ||||||
|
MUMA Resource Report Resource Website 10+ mentions |
MUMA (RRID:SCR_002412) | MUMA | software application, software resource, standalone software | Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY). | standalone software, mac os x, unix/linux, windows, r, metabolomics, univariate, multivariate, data analysis |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_03370 | SCR_002412 | Metabolomics Univariate and Multivariate Analysis (MUMA), Metabolomic Univariate and Multivariate Analysis | 2026-09-05 06:32:26 | 28 | |||||||
|
nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, software resource, standalone software | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Edelman-Gardner Foundation ; NCI CA009363; NCI CA138249; NHGRI HG006853 |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-09-05 06:32:25 | 1 | |||||
|
enviPick Resource Report Resource Website 1+ mentions |
enviPick (RRID:SCR_003059) | software resource, web site | Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_05010 | https://rdrr.io/cran/enviPick/ | SCR_003059 | enviPick: Peak picking for high resolution mass spectrometry data | 2026-09-05 06:32:29 | 2 |
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