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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Treephyler Resource Report Resource Website 1+ mentions |
Treephyler (RRID:SCR_000109) | Treephyler | software resource | A software tool for fast taxonomic profiling of metagenomes. | metagenome, perl, nucleotide, protein, next-generation sequencing | is listed by: OMICtools | PMID:20172941 | Free, Available for download, Freely available | OMICS_01469 | SCR_000109 | Treephyler: fast taxonomic profiling of metagenomes | 2026-02-07 02:05:17 | 1 | ||||||
|
GenomicRanges Resource Report Resource Website 10+ 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 | 2026-02-07 02:05:16 | 47 | |||||||
|
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 | 2026-02-07 02:05:17 | 1 | |||||||
|
DOCK Resource Report Resource Website 10+ mentions |
DOCK (RRID:SCR_000128) | DOCK | software resource | An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design. | molecule docking, ligand model, drug design, molecular biology |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Available to the research community, Free for the academic community, License fee for industrial organizations, Available for download | OMICS_01598 | SCR_000128 | UCSF DOCK | 2026-02-07 02:05:17 | 16 | |||||||
|
exomeSuite Resource Report Resource Website |
exomeSuite (RRID:SCR_000129) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease. | standalone software, c, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24603341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04839 | SCR_000129 | 2026-02-07 02:05:19 | 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 | 2026-02-07 02:05:16 | 0 | ||||||||
|
nFuse Resource Report Resource Website 1+ mentions |
nFuse (RRID:SCR_000066) | nFuse | software resource | Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS). | cancer, genomics |
is listed by: OMICtools is listed by: Google Code has parent organization: Simon Fraser University; British Columbia; Canada |
Cancer | PMID:22745232 | Free, Available for download, Freely available, | OMICS_01353 | SCR_000066 | nFuse: Discovery of Complex Genomic Rearrangements in Cancer | 2026-02-07 02:05:16 | 2 | |||||
|
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 | 2026-02-07 02:05:17 | 5 | |||||
|
PSGInfer Resource Report Resource Website |
PSGInfer (RRID:SCR_000243) | PSGInfer | software resource | Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. | alternative splicing, rna-seq, probabilistic splice graph |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:23846746 | Free, Available for download, Freely available | OMICS_01967 | SCR_000243 | PSGInfer: Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs | 2026-02-07 02:05:20 | 0 | ||||||
|
Cascleave Resource Report Resource Website |
Cascleave (RRID:SCR_000197) | Cascleave | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates. | matlab |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24149049 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01670 | SCR_000197 | Cascleave 2.0 - Caspase substrate cleavage site prediction, Cascleave 2.0 | 2026-02-07 02:05:20 | 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 | 2026-02-07 02:05:18 | 0 | ||||||
|
Molegro Virtual Docker Resource Report Resource Website 1+ mentions |
Molegro Virtual Docker (RRID:SCR_000190) | Molegro Virtual Docker | software resource | An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets. | protein ligand, protein target, visualization, integrated platform | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01603 | SCR_000190 | 2026-02-07 02:05:18 | 9 | ||||||||
|
MRNet Resource Report Resource Website 1+ mentions |
MRNet (RRID:SCR_000225) | MRNet | software resource | A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication. | is listed by: OMICtools | DOI:10.1145/1048935.1050172 | Free, Available for download, Freely available | OMICS_01686 | SCR_000225 | MRNet: A Multicast/Reduction Network | 2026-02-07 02:05:19 | 1 | |||||||
|
FastQ Screen Resource Report Resource Website 10+ mentions |
FastQ Screen (RRID:SCR_000141) | FastQ Screen | software resource | Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. | perl, FASEB list |
is listed by: OMICtools has parent organization: Babraham Institute |
PMID:30254741 | Free, Available for download, Freely available | OMICS_01042 | SCR_000141 | 2026-02-07 02:05:19 | 47 | |||||||
|
MS-Spectre Resource Report Resource Website 1+ mentions |
MS-Spectre (RRID:SCR_000266) | software resource | Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02496 | SCR_000266 | Mass Spectrometry Analysis Software | 2026-02-07 02:05:19 | 1 | ||||||||
|
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) | 2026-02-07 02:05:19 | 15 | |||||
|
BLASTPLOT Resource Report Resource Website |
BLASTPLOT (RRID:SCR_000162) | BLASTPLOT | software resource | A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set. | perl, blast, short sequence, primer, png, png graph |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24685334 | Free, Available for download, Freely available | OMICS_01433 | SCR_000162 | 2026-02-07 02:05:20 | 0 | |||||||
|
GemSIM Resource Report Resource Website |
GemSIM (RRID:SCR_000167) | GemSIM | software resource | A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface. | bioinformatics, simulation, sequencing, dna, rna, empirical models, Python, command-line, user interface, metagenomic, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: Wessim |
PMID:22336055 DOI:10.1186/1471-2164-13-74 |
Free, Available for download, Freely available | OMICS_01507, biotools:GemSIM | https://bio.tools/GemSIM | SCR_000167 | 2026-02-07 02:05:20 | 0 | ||||||
|
iFad Resource Report Resource Website |
iFad (RRID:SCR_000271) | iFad | software resource | An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines. | r, gene expression, drug sensitivity, analysis, drug-pathway association, gene-pathway, pathway, gene, drug |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:22581178 | Free, Available for download, Freely available | OMICS_01959 | SCR_000271 | 2026-02-07 02:05:18 | 0 | |||||||
|
GramCluster Resource Report Resource Website |
GramCluster (RRID:SCR_000272) | GramCluster | software resource | Software implementing a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets. | 16s sequence, cluster |
is listed by: OMICtools has parent organization: University of Nebraska; Nebraska; USA |
PMID:21167044 | Free, Available for download, Freely available | OMICS_01956 | SCR_000272 | 2026-02-07 02:05:20 | 0 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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 Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
