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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-12 12:55:39 | 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 | 2026-09-12 12:55:38 | 376 | |||||||
|
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 | 2026-09-12 12:55:03 | 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 | 2026-09-12 12:55:02 | 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 | 2026-09-12 12:55:02 | 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 | 2026-09-12 12:55:03 | 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 | 2026-09-12 12:55:02 | 6 | |||||
|
MIMOSA Resource Report Resource Website |
MIMOSA (RRID:SCR_000184) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23887981 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mimosa, OMICS_05642 | https://bio.tools/mimosa | SCR_000184 | MIMOSA - Mixture Models for Single-Cell Assays, MIMOSA: Mixture Models For Single Cell Assays | 2026-09-12 12:55:04 | 0 | ||||||
|
iASeq Resource Report Resource Website |
iASeq (RRID:SCR_000420) | software resource | Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. | software package, unix/linux, mac os x, windows, r, chip-seq, rna-seq, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23194258 | Free, Available for download, Freely available | OMICS_05505 | SCR_000420 | iASeq: integrating multiple sequencing datasets for detecting allele-specific events | 2026-09-12 12:55:09 | 0 | |||||||
|
rTANDEM Resource Report Resource Website |
rTANDEM (RRID:SCR_000409) | software resource | An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics |
is used by: shinyTANDEM is listed by: OMICtools has parent organization: Bioconductor |
PMID:24700319 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03516 | SCR_000409 | rTANDEM - Interfaces the tandem protein identification algorithm in R | 2026-09-12 12:55:08 | 0 | |||||||
|
flowPeaks Resource Report Resource Website |
flowPeaks (RRID:SCR_000407) | software resource | Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gating, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22595209 | Free, Available for download, Freely available | biotools:flowpeaks, OMICS_05604 | http://www.bioconductor.org/packages/devel/bioc/html/flowPeaks.html, https://bio.tools/flowpeaks | SCR_000407 | 2026-09-12 12:55:08 | 0 | |||||||
|
QUALIFIER Resource Report Resource Website |
QUALIFIER (RRID:SCR_000389) | software resource | Software that provides quality control and quality assessment tools for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05618 | SCR_000389 | QUALIFIER - Quality Control of Gated Flow Cytometry Experiments | 2026-09-12 12:55:08 | 0 | |||||||
|
sybil - Efficient Constrained Based Modelling in R Resource Report Resource Website |
sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) | sybil | software resource | A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language. | unix/linux, windows, r |
is listed by: OMICtools is related to: SBML is related to: CRAN |
PMID:24224957 | Free, Available for download, Freely available | OMICS_06008 | http://www.cs.hhu.de/en/research-groups/bioinformatics/software/sybil.html | http://cran.r-project.org/web/packages/sybil/index.html | SCR_000457 | sybil: sybil - Efficient Constrained Based Modelling in R | 2026-09-12 12:55:09 | 0 | ||||
|
Rdisop Resource Report Resource Website |
Rdisop (RRID:SCR_000453) | software resource | Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02416, biotools:rdisop | https://github.com/sneumann/Rdisop, https://bio.tools/rdisop | SCR_000453 | Rdisop - Decomposition of Isotopic Patterns, Rdisop: Decomposition of Isotopic Patterns, Decomposition of Isotopic Patterns | 2026-09-12 12:55:09 | 0 | |||||||
|
FlipFlop Resource Report Resource Website |
FlipFlop (RRID:SCR_000625) | software resource | Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. | standalone software, unix/linux, mac os x, windows, r, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24813214 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04028, biotools:flipflop | https://bio.tools/flipflop | SCR_000625 | flipflop - Fast lasso-based isoform prediction as a flow problem | 2026-09-12 12:55:12 | 0 | ||||||
|
RMassBank Resource Report Resource Website 1+ mentions |
RMassBank (RRID:SCR_002797) | data processing software, software application, software resource, workflow software | Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02657 | SCR_002797 | 2026-09-12 01:00:35 | 9 | |||||||||
|
NMR metabolomics database of Linkoping Resource Report Resource Website 1+ mentions |
NMR metabolomics database of Linkoping (RRID:SCR_002758) | MDL | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules. | nuclear magnetic resonance, metabolomics, mac os x, unix/linux, windows |
is listed by: OMICtools has parent organization: Linkoping University; Linkoping; Sweden |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02853 | SCR_002758 | MDL - The Magnetic Resonance Metabolomics Database, Magnetic Resonance Metabolomics Database | 2026-09-12 01:01:26 | 1 | |||||||
|
skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | data processing software, software application, software resource | Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences. | illumina, unix/linux, c++, adapter trimming, paired-end, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24925680 | Free, Available for download, Freely available | OMICS_02106, biotools:skewer | https://bio.tools/skewer, https://sources.debian.org/src/skewer/, https://github.com/relipmoc/skewer | SCR_001151 | skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences | 2026-09-12 01:00:52 | 14 | |||||
|
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 | 2026-09-12 01:02:23 | 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 | 2026-09-12 01:02:28 | 2138 |
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