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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pseudomonas Genome Database Resource Report Resource Website 100+ mentions |
Pseudomonas Genome Database (RRID:SCR_006590) | PseudoCAP | data analysis service, data or information resource, database, service resource, production service resource, analysis service resource | Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download. | gene, genome, annotation, localization, prokaryote, pseudomonas aeruginosa, sequence, subcellular, cystic fibrosis, ortholog, annotation, dna sequence, intergenic dna, protein sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: Debian is listed by: bio.tools is related to: AmiGO has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada |
Cystic Fibrosis Foundation Therapeutics Inc | PMID:18978025 | nif-0000-03369, r3d100012086, biotools:pseudomonas_genome_database | https://bio.tools/pseudomonas_genome_database, https://doi.org/10.17616/R3935H | SCR_006590 | Pseudomonas Genome Database - Improving Disease Treatment Through Genome Research | 2026-07-31 09:26:25 | 489 | |||||
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Variant Effect Predictor Resource Report Resource Website 1000+ mentions |
Variant Effect Predictor (RRID:SCR_007931) | VEP | data analysis service, service resource, production service resource, software resource, analysis service resource | Data analysis service to predict the functional consequences of known and unknown variants. | perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ensembl |
biotools:ensembl_variant_effect_predictor | https://bio.tools/ensembl_variant_effect_predictor | SCR_007931 | Ve!P | 2026-07-31 09:26:36 | 1871 | |||||||
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eTBlast Resource Report Resource Website 1+ mentions |
eTBlast (RRID:SCR_008188) | eTBlast | narrative resource, data or information resource, database, service resource | eTBLAST is a unique search engine for searching biomedical literature. Our service is very different from PubMed. While PubMed searches for keywords, our search engine lets you input an entire paragraph and returns MEDLINE abstracts that are similar to it. This is something like PubMed''s Related Articles feature, only better because it runs on your unique set of interests. For example, input the abstract of an unpublished paper or a grant proposal into our engine, and with the touch of a button you''ll be able to find every abstract in MEDLINE dealing with your topic. No more guessing whether your set of keywords has found all the right papers. No more sorting through hundreds of papers you don''t care about to find the handful you were looking for--our search engine does it for you. When most people use PubMed to search MEDLINE they pick one or two keywords to describe their topic, then browse through a long list of results. When they find a paper that looks interesting they click on its Related Articles, in hopes of finding more papers like that one. If they find another relevant paper, they explore it''s related articles--and so on. This process of culling long lists of documents by hand makes literature searching tedious and time consuming. We make it easier for you by providing better results the first time, and then allowing you to automatically combine the papers you care about for a second round. Our Iterate feature allows you to checkmark the abstracts you found interesting in the first round and combine them all to create a new query. It''s like rolling several Related Articles lists into one. * We sort our results by relevance, while PubMed sorts by date. * We save you the time and effort of creating a complicated query. * We let you iterate your search over several good papers to narrow your focus. * We provide you the full MEDLINE abstract in our results, and a link to the PubMed page. * We can send your results straight to your email so you never lose a reference or forget where you found it. * This absolutely free service is provided by the University of Texas Southwestern Medical Center. No registration necessary! | biomedical, literature, medline interfaces, paper, publish, search engine, unpublished, journal, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
Hudson Foundation ; P.O'B. Montgomery Distinguished Chair |
PMID:16926219 | biotools:etblast, nif-0000-21148 | https://bio.tools/etblast | http://invention.swmed.edu/etblast/index.shtml | SCR_008188 | eTBLAST: a text-similarity based search engine | 2026-07-31 09:26:43 | 4 | ||||
|
tRNAscan-SE Resource Report Resource Website 1000+ mentions |
tRNAscan-SE (RRID:SCR_008637) | data analysis service, web application, service resource, production service resource, software resource, analysis service resource | Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file). | bio.tools, tRNA genes, genomic sequence |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:15980563 PMID:9023104 DOI:10.1093/nar/25.5.0955 |
Free, Freely available | SCR_010835, OMICS_00385, nif-0000-32031, biotools:trnascan-se | https://bio.tools/trnascan-se, https://sources.debian.org/src/trnascan-se/ | SCR_008637 | Lowe Lab tRNAscan-SE | 2026-07-31 09:26:41 | 2493 | ||||||
|
Network Analysis, Visualization and Graphing TORonto Resource Report Resource Website 50+ mentions |
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) | NAViGaTOR | data visualization software, software application, data processing software, d visualization software, software resource | A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. | fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Genomics Institute ; Canada Research Chair Program ; Ontario Research Fund Research Excellence ; Canada Foundation for Innovation 12301; Canada Foundation for Innovation 203383 |
PMID:19837718 | Freely-downloadable for academic and not-for-profit institutions | nif-0000-25610, biotools:navigator | https://bio.tools/navigator | SCR_008373 | NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto | 2026-07-31 09:26:39 | 52 | ||||
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EMBOSS Resource Report Resource Website 1000+ mentions |
EMBOSS (RRID:SCR_008493) | EMBOSS | software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication. | FASEB list |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: BioExtract is related to: pepwheel |
DOI:10.1016/S0168-9525(00)02024-2 | Free, Freely available | OMICS_21165, nif-0000-30488 | https://sources.debian.org/src/emboss/ | http://www.emboss.org | SCR_008493 | The European Molecular Biology Open Software Suite, European Molecular Biology Open Software Suite | 2026-07-31 09:26:40 | 4543 | ||||
|
Vienna RNA Resource Report Resource Website 100+ mentions |
Vienna RNA (RRID:SCR_008550) | software resource, data or information resource, database | This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Vienna; Vienna; Austria |
DOI:10.1186/1748-7188-6-26 | biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 | https://bio.tools/vienna_rna_package, https://sources.debian.org/src/vienna-rna/ | SCR_008550 | Vienna RNA | 2026-07-31 09:26:50 | 404 | |||||||
|
GMAP Resource Report Resource Website 500+ mentions |
GMAP (RRID:SCR_008992) | GMAP | image analysis software, alignment software, source code, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. | mrna, est sequence, expressed sequence tag, sequence, cdna sequence, genome, cdna, bio.tools |
is used by: deFuse is listed by: Debian is listed by: bio.tools has parent organization: Genentech |
PMID:15728110 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15072, biotools:gmap, nlx_152505 | https://bio.tools/gmap, https://sources.debian.org/src/gmap/ | SCR_008992 | 2026-07-31 09:26:45 | 594 | ||||||
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STEPS Resource Report Resource Website 100+ mentions |
STEPS (RRID:SCR_008742) | STEPS | software resource, software application, simulation software | STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on Gillespie''s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution. | reaction-diffusion, stochastic, signaling, molecular, python, software, simulator, reaction kinetics, 3d diffusion, signaling pathway, scripting, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Okinawa Institute of Science and Technology has parent organization: University of Antwerp; Antwerp; Belgium |
GOA ; UA Belgium ; Human Frontier Science Program ; Okinawa Institute of Science and Technology |
biotools:steps, nlx_143852 | https://bio.tools/steps | http://steps.sourceforge.net/STEPS/Home.html | SCR_008742 | STochastic Engine For Pathway Simulation | 2026-07-31 09:26:42 | 336 | |||||
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NetOGlyc Resource Report Resource Website 500+ mentions |
NetOGlyc (RRID:SCR_009026) | NetOGlyc | data analysis service, service resource, software application, production service resource, software resource, analysis service resource | Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. | neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CBS Prediction Servers |
PMID:23584533 | Acknowledgement requested | nlx_153864, biotools:netoglyc | https://bio.tools/netoglyc | SCR_009026 | NetOGlyc Server | 2026-07-31 09:26:59 | 601 | |||||
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elastix Resource Report Resource Website 100+ mentions |
elastix (RRID:SCR_009619) | elastix | image analysis software, software toolkit, software application, data processing software, registration software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | reusable library, analyze, c++, console (text based), domain independent, nifti, nrrd, os independent, philips par/rec, registration, resampling, spatial transformation, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is related to: Insight Segmentation and Registration Toolkit has parent organization: Utrecht University; Utrecht; Netherlands |
PMID:19923044 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155845, biotools:elastix | http://www.nitrc.org/projects/elastix, https://bio.tools/elastix, https://sources.debian.org/src/elastix/ | SCR_009619 | 2026-07-31 09:26:48 | 167 | ||||||
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BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software resource, software application | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-07-31 09:26:45 | 39 | ||||||
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IMGT-ONTOLOGY Resource Report Resource Website |
IMGT-ONTOLOGY (RRID:SCR_010342) | IMGT-ONTOLOGY | ontology, controlled vocabulary, data or information resource | Ontology for immunogenetics and immunoinformatics. Provides semantic specification of terms to be used in immunogenetics and immunoinformatics and manages related knowledge, thus allowing standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. Manages the knowledge through diverse facets relying on seven axioms, IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, LOCALIZATION, ORIENTATION and OBTENTION. These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT, the international ImMunoGeneTics information system, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION. | owl, ontology, immunogenetics, immunoinformatics, terms semantic specification, bio.tools |
is listed by: BioPortal is listed by: Debian is listed by: bio.tools has parent organization: IMGT - the international ImMunoGeneTics information system |
Free, Freely available | nlx_157436, biotools:IMGt-ONtOLOGY | http://www.imgt.org/IMGTindex/ontology.php, https://bio.tools/IMGT-ONTOLOGY | SCR_010342 | 2026-07-31 09:27:06 | 0 | |||||||
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PSIPRED Resource Report Resource Website 1000+ mentions |
PSIPRED (RRID:SCR_010246) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences. | Predict Secondary Structure, protein analysis, secondary structure prediction, protein sequence, sequence analysis, protein, analysis |
is listed by: Debian is listed by: SoftCite has parent organization: University College London; London; United Kingdom |
Biotechnology and Biological Science Research Council ; University College London |
DOI:10.1093/nar/gkz297 | Free, Freely available | SCR_018546, nlx_156884 | https://sources.debian.org/src/psipred/ | SCR_010246 | PSIPRED Protein Sequence Analysis Workbench, PSIPRED 4.0 | 2026-07-31 09:27:05 | 1688 | |||||
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Evex Resource Report Resource Website 10+ mentions |
Evex (RRID:SCR_010509) | data or information resource, text-mining software, database, software application, software resource | EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. | gene, protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium |
biotools:evex, nlx_158731 | https://bio.tools/evex | SCR_010509 | 2026-07-31 09:26:55 | 18 | |||||||||
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | software resource, data access protocol, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-07-31 09:24:52 | 16 | |||||
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nmrML Resource Report Resource Website 1+ mentions |
nmrML (RRID:SCR_000467) | nmrML | data or information resource, markup language, narrative resource, standard specification, interchange format | An open mark-up language for NMR data. | nuclear magnetic resonance, bio.tools |
is listed by: bio.tools is listed by: Debian is parent organization of: nmrCV |
nlx_157309, biotools:nmrml_converter | https://bio.tools/nmrml_converter | SCR_000467 | 2026-07-31 09:24:55 | 9 | ||||||||
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CovalentDock Cloud Resource Report Resource Website |
CovalentDock Cloud (RRID:SCR_000126) | CovalentDock Cloud | software resource, data access protocol, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor. | protein ligand covalent docking, ligand, receptor, covalent linkage, data analysis service, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23034731 | THIS RESOURCE IS NO LONGER IN SERVICE | covalentdock_cloud, OMICS_01597 | https://bio.tools/covalentdock_cloud | SCR_000126 | 2026-07-31 09:24:51 | 0 | ||||||
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cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | software toolkit, data analysis software, software application, data processing software, software resource | Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. | copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:21486749 | Free, Available for download, Freely available | biotools:cn.farms, OMICS_02060 | https://bio.tools/cn.farms | SCR_000289 | cn.farms - factor analysis for copy number estimation | 2026-07-31 09:24:52 | 0 | |||||
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Dipy Resource Report Resource Website 10+ mentions |
Dipy (RRID:SCR_000029) | DIPY | software toolkit, data analysis software, software application, data processing software, software resource | Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data. | MRI, magnetic resonance, diffusion data analysis, diffusion MRI data, diffusion MRI data analysis, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Neuroimaging in Python has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:24600385 | Free, Available for download, Freely available | nlx_155745 | https://sources.debian.org/src/python-dipy/, http://www.nitrc.org/projects/dipy, http://elef.soic.indiana.edu/, https://github.com/nipy/dipy_web, | http://nipy.org/dipy/ | SCR_000029 | Diffusion Imaging In Python, NIPY Diffusion Imaging Analysis | 2026-07-31 09:24:49 | 15 |
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