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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
eisa Resource Report Resource Website 1+ mentions |
eisa (RRID:SCR_012883) | eisa | software resource | A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free | OMICS_01801, biotools:eisa | https://bio.tools/eisa | SCR_012883 | eisa - Expression data analysis via the Iterative Signature Algorithm | 2026-09-19 12:52:34 | 2 | ||||||
|
GeneProf Resource Report Resource Website 10+ mentions |
GeneProf (RRID:SCR_012927) | GeneProf | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | A database of curated, integrated and reusable high-throughput genomics experiments and a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; Next-Generation Sequencing or NGS). Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework and data from GeneProf may be used externally. | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Edinburgh; Scotland; United Kingdom |
MRC ; European Union Framework 7 Project EuroSyStem |
PMID:22205509 PMID:24174536 |
Acknowledgement requested | biotools:geneprof, OMICS_00442 | https://bio.tools/geneprof | SCR_012927 | 2026-09-19 12:52:35 | 15 | |||||
|
Trowel Resource Report Resource Website 1+ mentions |
Trowel (RRID:SCR_012890) | Trowel | software resource | An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. | c++, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Apache License | OMICS_01111, biotools:trowel | https://bio.tools/trowel/ | SCR_012890 | Trowel - Error Correction Module for Illumina Sequencing Reads, Trowel - Sequencing Error Corrector | 2026-09-19 12:52:34 | 5 | ||||||
|
CSAR Resource Report Resource Website 50+ mentions |
CSAR (RRID:SCR_012930) | CSAR | software resource | Statistical tools for the analysis of ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21554688 | Free | OMICS_00435, biotools:csar | https://bio.tools/csar | SCR_012930 | 2026-09-19 12:52:35 | 50 | ||||||
|
SeqPrep Resource Report Resource Website 1000+ mentions |
SeqPrep (RRID:SCR_013004) | SeqPrep | software resource | A program to merge paired end Illumina reads that are overlapping into a single longer read. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
biotools:seqprep, OMICS_01092 | https://bio.tools/seqprep, https://sources.debian.org/src/seqprep/ | SCR_013004 | SeqPrep - Tool for stripping adaptors and/or merging paired reads with overlap into single reads | 2026-09-19 12:52:36 | 1146 | |||||||
|
phyloseq Resource Report Resource Website 1000+ mentions |
phyloseq (RRID:SCR_013080) | phyloseq | software resource | Software for handling and analysis of high-throughput microbiome census data. | bio.tools |
is used by: microViz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1371/journal.pone.0061217 | OMICS_01520, biotools:phyloseq | https://bio.tools/phyloseq, https://sources.debian.org/src/r-bioc-phyloseq/ | SCR_013080 | 2026-09-19 12:52:38 | 3080 | |||||||
|
QuantiSNP Resource Report Resource Website 50+ mentions |
QuantiSNP (RRID:SCR_013091) | QuantiSNP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development. | matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17341461 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:quantisnp, OMICS_00730 | https://bio.tools/quantisnp | SCR_013091 | 2026-09-19 12:52:38 | 83 | ||||||
|
AMOS Resource Report Resource Website 1000+ mentions |
AMOS (RRID:SCR_013067) | AMOS | software resource | A collection of tools and class interfaces for the assembly of DNA reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1093/bib/bbr074 | OMICS_00008, biotools:amos | https://bio.tools/amos, https://sources.debian.org/src/ampliconnoise/ | SCR_013067 | 2026-09-19 12:52:38 | 4855 | |||||||
|
Reptile Resource Report Resource Website 10+ mentions |
Reptile (RRID:SCR_013075) | Reptile | software resource | A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20834037 | biotools:reptile, OMICS_01109 | https://bio.tools/reptile | SCR_013075 | 2026-09-19 12:52:38 | 30 | |||||||
|
IUPHAR/BPS Guide to Pharmacology Resource Report Resource Website 1000+ mentions |
IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) | IUPHAR Database, IUPHAR-DB, IUPHAR GPCR, IUPHAR RECEPTOR | data or information resource, database, narrative resource, portal, standard specification | Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. | pharmacology, drug discovery, portal, guide, physiology, molecular structure, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: NC-IUPHAR |
Wellcome Trust | PMID:21087994 | nif-0000-03056, biotools:iuphar-db, r3d100013308 | https://bio.tools/iuphar-db, https://doi.org/10.17616/R31NJMRG | http://www.iuphar-db.org | SCR_013077 | International Union of Pharmacology Database, International Union of Basic and Clinical Pharmacology Database | 2026-09-19 12:52:38 | 2375 | ||||
|
FluoRender Resource Report Resource Website 100+ mentions |
FluoRender (RRID:SCR_014303) | data analysis software, data processing software, data visualization software, software application, software resource | Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation. | rendering tool, confocal microscopy data visualization, neurobiology, fluorescent stain, brain, bio.tools |
is used by: VVD Viewer is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
Free, Available for download, Freely available | biotools:fluorender | https://bio.tools/fluorender | SCR_014303 | FluoRender Visualization | 2026-09-19 12:52:55 | 130 | |||||||
|
NiftyFit Resource Report Resource Website 10+ mentions |
NiftyFit (RRID:SCR_014301) | software library, software resource, software toolkit | Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T | software library, voxel wise fit, relaxometry, mri, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
EPSRC ; MRC ; NIHR BRC ; NIHR |
PMID:26972806 | Free, Available for download, Freely available | biotools:niftyfit, BioTools:niftyfit | https://github.com/KCL-BMEIS/niftyreg, https://bio.tools/niftyfit, https://bio.tools/niftyfit, https://bio.tools/niftyfit | SCR_014301 | 2026-09-19 12:52:55 | 14 | ||||||
|
SortMeRNA Resource Report Resource Website 500+ mentions |
SortMeRNA (RRID:SCR_014402) | data analysis software, data processing software, sequence analysis software, software application, software resource | Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis software, filter, map, otu picking, ngs, sort, rna, rrna, bio.tools |
uses: QIIME is listed by: Debian is listed by: bio.tools |
PMID:23071270 DOI:10.1093/bioinformatics/bts611 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02619, biotools:sortmerna | https://bio.tools/sortmerna, https://sources.debian.org/src/sortmerna/ | SCR_014402 | 2026-09-19 12:52:56 | 624 | |||||||
|
Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | data processing software, signal processing software, software application, software resource, standalone software | A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters. | server, software package, mass spectrometry, protein, identify, characterize, bio.tools |
is used by: MSQuant is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MascotScan |
Free, Can be licensed for in-house use, Available for download | biotools:MASCOT | http://www.matrixscience.com/search_intro.html, https://bio.tools/MASCOT | SCR_014322 | Mascot Server | 2026-09-19 12:52:55 | 7141 | |||||||
|
OpenWorm Resource Report Resource Website 10+ mentions |
OpenWorm (RRID:SCR_014650) | simulation software, software application, software resource, web application | 3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders. | simulation, model, web application, web browser, c elegans, nematode, worm, roundworm, open source, 3d, dissect, anatomy, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: WormBase is hosted by: GitHub |
PMID:25404913 DOI:10.3389/fncom.2014.00137 |
Open source, Code is available on GitHub, Available on the App Store | SCR_014984, biotools:OpenWorm | https://bio.tools/OpenWorm | SCR_014650 | OpenWorm Browser, Open Worm | 2026-09-19 12:53:00 | 21 | ||||||
|
ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | data analysis software, data processing software, software application, software resource, web application | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3, https://bio.tools/prottest, https://sources.debian.org/src/prottest/ | SCR_014628 | 2026-09-19 12:53:00 | 1984 | |||||||
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | software resource, web application | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-09-19 12:53:00 | 139 | |||||
|
CummeRbund Resource Report Resource Website 100+ mentions |
CummeRbund (RRID:SCR_014568) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions. | r software, cufflink, rna-seq, sqlite, gene, transcript, transcription start site, cds region, r, rnaseq, rna seq, bio.tools, FASEB list |
uses: R Project for Statistical Computing is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard University; Cambridge; United States |
Free, Freely available | biotools:cummerbund, OMICS_07349 | https://bio.tools/cummerbund, https://sources.debian.org/src/r-bioc-cummerbund/ | SCR_014568 | 2026-09-19 12:52:58 | 366 | ||||||||
|
ggplot2 Resource Report Resource Website 10000+ mentions |
ggplot2 (RRID:SCR_014601) | data processing software, data visualization software, software application, software resource | Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers. | plotting system, r, graphics, data analysis, multi-layered graphics, bio.tools |
uses: ggpubr uses: ggeffects uses: ggsignif is used by: riboWaltz is used by: ClustVis is used by: ggrepel is used by: PlotsOfData is used by: EnhancedVolcano is used by: tidyverse is used by: ComplexUpset is used by: ggfortify is used by: forestmodel is used by: ggvenn is used by: metaviz is used by: ggVennDiagram is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: ggraph is related to: ggbiplot is related to: GGally is related to: ggstatsplot is related to: ggpointdensity has parent organization: CRAN works with: Plotly works with: cowplot works with: ggalluvial works with: ggforce works with: ggbreak works with: ggrastr works with: tidybayes works with: ggsurvfit works with: ggtext works with: ggsci |
Free, Freely available | biotools:ggplot2 | http://docs.ggplot2.org/current/, https://github.com/tidyverse/ggplot2, https://bio.tools/ggplot2 | http://ggplot2.org/ | SCR_014601 | grammar of graphics plot2 | 2026-09-19 12:52:59 | 42192 | ||||||
|
Metastats Resource Report Resource Website 100+ mentions |
Metastats (RRID:SCR_014610) | data analysis software, data processing software, software application, software resource, web application | A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test. | microbiome, statistics, software, metagenomics, clinical data, data analysis software, machine learning, web application, bio.tools |
is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian |
Open source, Acknowledgement requested | biotools:metastats | https://bio.tools/metastats | SCR_014610 | 2026-09-19 12:52:59 | 390 |
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