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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Agile Protein Interactomes DataServer
 
Resource Report
Resource Website
10+ mentions
Agile Protein Interactomes DataServer (RRID:SCR_008871) APID analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. protein, protein interaction, interactions, ppi, interactomes, analysis, gene, ontology, functional, environment, data, network, graphic, visualize is listed by: Gene Ontology Tools
is related to: PSICQUIC Registry
is related to: Gene Ontology
is related to: BIND
is related to: Biological General Repository for Interaction Datasets (BioGRID)
is related to: Database of Interacting Proteins (DIP)
is related to: HPRD - Human Protein Reference Database
is related to: IntAct
is related to: MINT
has parent organization: University of Salamanca; Salamanca; Spain
Junta de Castilla y Leon ;
Spanish Ministerio de Sanidad y Consumo
PMID:27131791
PMID:30715274
Free for academic use r3d100012339, nlx_149321 https://doi.org/10.17616/R3407P, https://doi.org/10.17616/R3407P SCR_008871 Agile Protein Interactomes DataServer, APID, APID Interactomes, Agile Protein Interactomes DataServer (APID), APID (Agile Protein Interactomes DataServer) 2026-09-03 04:49:48 14
GMA
 
Resource Report
Resource Website
GMA (RRID:SCR_009212) GMA data analysis software, data processing software, software application, software resource, time-series analysis software Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. Granger, meditation, analysis, time, series, level, GMA, model, BRAIN Initiative, bio.tools is recommended by: BRAIN Initiative
is listed by: Genetic Analysis Software
is listed by: Debian
is listed by: bio.tools
NIBIB EB022911 PMID:31070732 Free, Available for download, Freely available nlx_154361, biotools:GMA https://github.com/chaoning/GMA, https://bio.tools/GMA http://www.montana.edu/kalinowski/GMA/GMA_Home.htm SCR_009212 Granger Mediation Analysis 2026-09-03 04:49:53 0
Neural Decoding Toolbox
 
Resource Report
Resource Website
10+ mentions
Neural Decoding Toolbox (RRID:SCR_009012) NDT data analysis software, data processing software, software application, software resource, software toolkit Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. population decoding, neuron, analysis, matlab, data analysis, machine learning, multivariate pattern analysis, neural decoding has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; DARPA ;
IPTO ;
DSO ;
AFSOR-THRL ;
Adobe Systems ;
Honda Research Institute USA ;
King Abdullah University of Science and Technology ;
NEU ;
Sony ;
Eugene McDermott Foundation ;
NSF 0640097;
NSF 0827427;
NSF FA8650-05-C-7262
PMID:23734125 Acknowledgement requested, Account required nlx_152729 SCR_009012 2026-09-03 04:50:08 19
affy
 
Resource Report
Resource Website
1000+ mentions
affy (RRID:SCR_012835) Affy data analysis software, data processing software, software application, software resource Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools is listed by: OMICtools
is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: affydata
is related to: R Project for Statistical Computing
is related to: OMICtools
Danish Biotechnology Instrument Center PMID:14960456 Free, Available for download, Freely available BioTools:affy, OMICS_00740, biotools:affy https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ SCR_012835 Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data 2026-09-03 04:51:55 3073
TopHat
 
Resource Report
Resource Website
5000+ mentions
Rating or validation data
TopHat (RRID:SCR_013035) alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools uses: Bowtie
is used by: CIRCexplorer
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: HISAT2
has parent organization: University of Maryland; Maryland; USA
has parent organization: University of California at Berkeley; Berkeley; USA
has parent organization: Johns Hopkins University; Maryland; USA
has parent organization: University of Washington; Seattle; USA
works with: GeneScissors
NHGRI R01 HG006102;
NHGRI R01 HG006677
PMID:23618408
PMID:19289445
DOI:10.1093/bioinformatics/btp120
Free, Available for download, Freely available biotools:tophat, OMICS_01257 https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ http://tophat.cbcb.umd.edu/ SCR_013035 tophat, TopHat1, Tophat2 2026-09-03 04:51:54 9789
Neuroimaging in Python
 
Resource Report
Resource Website
10+ mentions
Neuroimaging in Python (RRID:SCR_013141) NIPY, community building portal, data or information resource, portal, software application, software development environment, software development tool, software resource Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Python Programming Language
has parent organization: SourceForge
has parent organization: University of California at Berkeley; Berkeley; USA
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
is parent organization of: Dipy
is parent organization of: NiLearn
is parent organization of: NIPY
is parent organization of: NiBabel
is parent organization of: Nipype
is parent organization of: Nitime
NIMH 5R01MH081909-02;
NIBIB 1R03EB008673-01
PMID:21897815 Revised BSD license nlx_149365 http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype SCR_013141 NIPY Community 2026-09-03 04:52:07 27
PlasmoDB
 
Resource Report
Resource Website
1000+ mentions
PlasmoDB (RRID:SCR_013331) analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list uses: SynView
is related to: GeneDB Pfalciparum
has parent organization: Eukaryotic Pathogen Database Resources
has parent organization: Pennsylvania State University
has parent organization: University of Georgia; Georgia; USA
malaria NIAID PMID:18957442 nif-0000-03314, SCR_017665, r3d100011569 SCR_013331 PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource 2026-09-03 04:51:57 1324
Leica Application Suite X
 
Resource Report
Resource Website
500+ mentions
Leica Application Suite X (RRID:SCR_013673) LAS X resource Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes. confocal, image, analysis, leica, microscope, microbiology has parent organization: Leica Microsystems Commercially available http://www.leica-microsystems.com/products/microscope-software/software-for-life-science-research/las-easy-and-efficient/ SCR_013673 Leica LAS, Leica LAS AF Image Acquisition Software, Leica Application Suite X, Leica Application Suite X (LAS X), Leica LAS X Life Science Microscope Software, Leica LAS X LS, LASX, Leica LAS X Life Science software, LAS X 2026-09-03 04:52:24 579
WinMDI Software
 
Resource Report
Resource Website
10+ mentions
WinMDI Software (RRID:SCR_013745) Software to analyze flow cytometry listmode data files. flow cytometry, analysis http://facs.scripps.edu/software.html SCR_013745 Windows Multiple Document Interface software, Windows Multiple Document Interface for Flow Cytometry 2026-09-03 04:52:14 28
InterProScan
 
Resource Report
Resource Website
5000+ mentions
InterProScan (RRID:SCR_005829) analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools is listed by: Gene Ontology Tools
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: Gene Ontology
is related to: RARTF
is related to: InterPro
is related to: LegumeIP
is related to: UniProtKB
has parent organization: European Bioinformatics Institute
Biotechnology and Biological Sciences Research Council ;
EMBL ;
European Union
PMID:15980438
PMID:17202162
PMID:24451626
Free, Available for download, Freely available OMICS_01479, biotools:interproscan_4, nlx_149337 https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 SCR_005829 InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 2026-09-03 04:48:39 7512
GOEx - Gene Ontology Explorer
 
Resource Report
Resource Website
10+ mentions
GOEx - Gene Ontology Explorer (RRID:SCR_005779) GOEx software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Scripps Research Institute
CNPq ;
CAPES ;
FAPERJ BBP grant ;
PAPES ;
PDTIS ;
Ary Frauzino Foundation ;
NIAID ;
NIH ;
genesis molecular biology laboratory ;
Fiocruz-INCA collaboration ;
NIAID UCSD/MCB0237059;
NCRR P41RR011823;
NIMH 5R01 MH067880
PMID:19239707 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149249 http://pcarvalho.com/patternlab/goex.shtml SCR_005779 Gene Ontology Explorer, GO Explorer 2026-09-03 04:48:15 32
Onto-Translate
 
Resource Report
Resource Website
1+ mentions
Onto-Translate (RRID:SCR_005725) Onto-Translate analysis service resource, data analysis service, data or information resource, database, production service resource, service resource In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Wayne State University; Michigan; USA
PMID:15215428 Free for academic use nlx_149182 SCR_005725 2026-09-03 04:48:05 3
Brede Toolbox
 
Resource Report
Resource Website
1+ mentions
Brede Toolbox (RRID:SCR_006204) Brede Toolbox data processing software, image analysis software, image processing software, software application, software resource A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is related to: Brede Database
is related to: Brede Database
is related to: Brede Wiki
has parent organization: THOR Center for Neuroinformatics
Free for academic use, Acknowledgement requested nif-0000-00275 SCR_006204 2026-09-03 04:48:20 1
Knime
 
Resource Report
Resource Website
500+ mentions
Knime (RRID:SCR_006164) KNIME data processing software, software application, software resource, software toolkit, text-mining software, workflow software KNIME (Konstanz Information Miner) is a user-friendly and comprehensive Open-Source data integration, processing, analysis, and exploration platform. KNIME (naim) is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualization and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. KNIME can be downloaded onto the desktop and used free of charge. KNIME products include additional functionalities such as shared repositories, authentication, remote execution, scheduling, SOA integration and a web user interface as well as world-class support. Robust big data extensions are available for distributed frameworks such as Hadoop. KNIME is used by over 3000 organizations in more than 60 countries. The modular data exploration platform, initially developed at the University of Konstanz, Germany, enables the user to visually create data flows, execute selected analysis steps, and later investigate the results through interactive views on data and models. KNIME is a proven integration platform for tools of numerous vendors due to its open and modular API. The KNIME.com product pipeline includes an Enterprise Server, Cluster Execution, Reporting solutions, and professional KNIME support subscriptions. KNIME.com also offer services such as data analysis, hands-on training and the development of customized components for KNIME. platform, next-generation sequencing, data analysis, visualization, selection, analysis, high-throughput screening, data mining, drug discovery has parent organization: University of Konstanz; Baden-Wurttemberg; Germany PMID:23110532
PMID:22644661
PMID:22607449
PMID:21984761
PMID:21873641
nlx_151666 SCR_006164 Konstanz Information Miner 2026-09-03 04:48:33 770
Array Studio
 
Resource Report
Resource Website
1+ mentions
Array Studio (RRID:SCR_010970) analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource, software toolkit Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data. Statistic, visualization, data, analysis, quantification, integrated environment, microarray data, RTPCR data, Taqman data, genotype data, copy number data, next generation sequencing data Free, Available for download, Freely available OMICS_00850 https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/ArrayStudio/ArrayStudio/ http://www.omicsoft.com/array-studio.php SCR_010970 2026-09-03 04:51:02 5
LIMMA
 
Resource Report
Resource Website
10000+ mentions
LIMMA (RRID:SCR_010943) LIMMA data analysis software, data processing software, software application, software resource Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. analysis, gene, expression, microarray, data, linear, model, bio.tools is used by: Glimma
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: GEO2R
is related to: Bioconductor
Free, Available for download, Freely available biotools:limma, OMICS_00769 https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ SCR_010943 Linear Models for Microarray Data 2026-09-03 04:50:33 27197
HOMER
 
Resource Report
Resource Website
5000+ mentions
HOMER (RRID:SCR_010881) HOMER data analysis software, data processing software, sequence analysis software, software application, software resource Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. motif, discovery, next, generation, sequencing, analysis, genomic, data is listed by: OMICtools
is related to: findMotif.pl
has parent organization: University of California at San Diego; California; USA
Foundation Leducq Transatlantic Network Grant ;
NCI CA52599;
NIDDK DK063491;
NIGMS P50 GM081892;
NIH HC088093;
NURSA consortium grant
PMID:20513432 OMICS_00483 http://biowhat.ucsd.edu/homer/index.html SCR_010881 HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 2026-09-03 04:50:30 5929
JCB DataViewer
 
Resource Report
Resource Website
10+ mentions
JCB DataViewer (RRID:SCR_002633) JCB DataViewer data or information resource, data repository, database, image repository, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot is listed by: FORCE11
is listed by: SoftCite
is related to: OME-TIFF Format
has parent organization: Rockefeller University; New York; USA
Glencoe Software ;
OME - Open Microscopy Environment
PMID:22869591 THIS RESOURCE IS NO LONGER IN SERVICE nlx_156057, r3d100010895 https://doi.org/10.17616/R3PW4G SCR_002633 2026-09-03 04:45:30 14
Rainbow
 
Resource Report
Resource Website
10+ mentions
Rainbow (RRID:SCR_002724) data analysis software, data processing software, sequence analysis software, software application, software resource Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:22942077
DOI:10.1093/bioinformatics/bts482
Free, Freely available, Available for download SCR_015992, OMICS_03722, biotools:rainbow https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ SCR_002724 RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq 2026-09-03 04:45:41 41
Time-series RNA-seq Analysis Package
 
Resource Report
Resource Website
1+ mentions
Time-series RNA-seq Analysis Package (RRID:SCR_002935) TRAP software resource A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. time-series, rna-seq, analysis is listed by: OMICtools
has parent organization: Seoul National University; Seoul; South Korea
PMID:24518221 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02590 SCR_002935 2026-09-03 04:46:00 3

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