Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ReQON Resource Report Resource Website |
ReQON (RRID:SCR_000075) | ReQON | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format. | preprocessing, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22946927 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02033 | SCR_000075 | Recalibrating Quality Of Nucleotides | 2026-02-14 01:59:36 | 0 | ||||||
|
GenomicRanges Resource Report Resource Website 50+ mentions |
GenomicRanges (RRID:SCR_000025) | GenomicRanges | software resource | Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. | genomic interval |
is used by: riboWaltz is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | SCR_018096, OMICS_01161 | SCR_000025 | GenomicRanges - Representation and manipulation of genomic intervals | 2026-02-14 01:59:35 | 50 | |||||||
|
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 | 2026-02-14 01:59:35 | 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 | 2026-02-14 01:59:37 | 0 | ||||||||
|
HEM Resource Report Resource Website |
HEM (RRID:SCR_000194) | HEM | software resource | Software package that fits heterogeneous error models for analysis of microarray data | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Virginia; Virginia; USA |
PMID:15044230 | Free, Available for download, Freely available | OMICS_01970 | SCR_000194 | HEM - Heterogeneous error model for identification of differentially expressed genes under multiple conditions | 2026-02-14 01:59:38 | 0 | ||||||
|
GEOquery Resource Report Resource Website 10+ mentions |
GEOquery (RRID:SCR_000146) | GEOquery | software resource | Software that establishes a bridge between GEO and BioConductor. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: GEO2R has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:17496320 | Free, Available for download, Freely available | biotools:geoquery, OMICS_01972 | https://bio.tools/geoquery https://sources.debian.org/src/r-bioc-geoquery/ |
SCR_000146 | GEOquery - Get data from NCBI Gene Expression Omnibus (GEO) | 2026-02-14 01:59:37 | 18 | |||||
|
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 | 2026-02-14 01:59:38 | 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 | 2026-02-14 01:59:43 | 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 | 2026-02-14 01:59:45 | 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 | 2026-02-14 01:59:43 | 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 | 2026-02-14 01:59:43 | 0 | |||||||
|
TDARACNE Resource Report Resource Website |
TDARACNE (RRID:SCR_000498) | TDARACNE | software resource | Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. | microarray, time course |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02013 | SCR_000498 | TDARACNE - Network reverse engineering from time course data | 2026-02-14 01:59:45 | 0 | |||||||
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-02-14 01:59:45 | 14 | |||||
|
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 | 2026-02-14 01:59:43 | 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 | 2026-02-14 01:59:50 | 0 | ||||||
|
Basic4Cseq Resource Report Resource Website 1+ mentions |
Basic4Cseq (RRID:SCR_002836) | software resource | An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. | software package, unix/linux, mac os x, windows, r, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25078398 | Free, Freely available, Available for download | OMICS_05202 | SCR_002836 | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data | 2026-02-14 02:00:19 | 6 | |||||||
|
mzR Resource Report Resource Website |
mzR (RRID:SCR_002856) | software resource | Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | standalone software, mac os x, unix/linux, windows, r, data import, infrastructure, mass spectrometry, metabolomics, proteomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02654 | SCR_002856 | mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files | 2026-02-14 02:00:33 | 0 | ||||||||
|
BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-02-14 02:00:33 | 0 | |||||||
|
PAPi Resource Report Resource Website 50+ mentions |
PAPi (RRID:SCR_002857) | software resource | An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20929912 | Free, Freely available, Available for download | OMICS_02653 | SCR_002857 | PAPi - Predict metabolic pathway activity based on metabolomics data, Pathway Activity Profiling | 2026-02-14 02:00:20 | 53 | |||||||
|
tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-02-14 02:00:29 | 4 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the ASWG Resources search. From here you can search through a compilation of resources used by ASWG and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that ASWG has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on ASWG then you can log in from here to get additional features in ASWG such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into ASWG you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the ASWG Community.
Our Information
