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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | data processing software, software application, software resource, source code | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip, https://sources.debian.org/src/phylip/ | SCR_006244 | SciCrunch Registry | PHYLogeny Inference Package | 2026-11-07 11:56:06 | 3544 | |||||
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ScerTF Resource Report Resource Website 10+ mentions |
ScerTF (RRID:SCR_006121) | ScerTF | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Catalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region. | binding site, transcription factor, regulatory site, gene, regulation, regulatory interaction, matrix, nucleotide sequence, dna sequence, yeast, position weight matrix, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIGMS R01 GM078222; NHGRI HG00249 |
PMID:22140105 | biotools:scertf, nlx_151599, OMICS_00542 | http://ural.wustl.edu/ScerTF, https://bio.tools/scertf | http://ural.wustl.edu/TFDB/ | SCR_006121 | SciCrunch Registry | 2026-11-07 11:56:05 | 19 | |||||
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SitEx Resource Report Resource Website 1+ mentions |
SitEx (RRID:SCR_006122) | SitEx | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms. | projection, protein, functional site, exon, blast, structure, function, gene, amino acid, encoding gene, proteome, ligand, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Ministry of Science and Education 14.740.11.0001; Ministry of Science and Education 07.514.11.4003; Interdisciplinary Integrative Project 35 of SB RAS ; Russian Foundation for Basic Research 11-04-92712; EU-FP7 260429; Program of RAS ; DAAD Leonard Euler Program Grant |
PMID:22139920 | THIS RESOURCE IS NO LONGER IN SERVICE. | biotools:sitex, nlx_151602 | https://bio.tools/sitex | SCR_006122 | SciCrunch Registry | SitEx Database | 2026-11-07 11:56:10 | 1 | ||||
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Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, source code | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | SciCrunch Registry | 2026-11-07 11:56:10 | 0 | |||||
|
Computerized Anatomical Reconstruction and Editing Toolkit Resource Report Resource Website 50+ mentions |
Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) | CARET | data processing software, data visualization software, image processing software, software application, software resource | Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems. | reconstruction, visualization, cerebral cortex, surface, brain, dataset, cerebellar cortex, atlas application, mesh generation, quantitative shape analysis, segmentation, shape analysis, intersubject, image-to-template, gaussian curvature, mean curvature, animation, three dimensional display, two dimensional display, surface rendering, cortical flat map, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SumsDB has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NEI EY02091; NIMH R01 MH60974 |
PMID:11522765 | Free, Available for download, Freely available | nif-0000-00279 | http://www.nitrc.org/projects/caret, https://sources.debian.org/src/caret/ | SCR_006260 | SciCrunch Registry | Computerized Anatomical Reconstruction Editing Toolkit | 2026-11-07 11:56:06 | 59 | ||||
|
SpliceDisease Resource Report Resource Website 1+ mentions |
SpliceDisease (RRID:SCR_006130) | SpliceDisease | data or information resource, data repository, database, service resource, storage service resource | Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser. | rna splicing, mutation, disease, gene, genomic sequence, nucleotide substitution, deletion, insertion, mutation location, splicing mutation, nucleotide, disease association, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 81001481 | PMID:22139928 | The community can contribute to this resource | biotools:splicedisease_db, nlx_151614 | https://bio.tools/splicedisease_db | SCR_006130 | SciCrunch Registry | Splice Disease, SpliceDisease Database Site, Splice Disease Database, SpliceDisease Database | 2026-11-07 11:55:49 | 2 | ||||
|
ChemSpider Resource Report Resource Website 1000+ mentions |
ChemSpider (RRID:SCR_006360) | ChemSpider | data access protocol, data or information resource, database, mobile app, service resource, software application, software resource, web service | Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications. | collection, chemical, structure, property, data, compound, bio.tools, FASEB list |
is used by: Open PHACTS is used by: GEROprotectors is listed by: re3data.org is listed by: bio.tools is listed by: Debian has parent organization: Royal Society of Chemistry |
GGA Software Services ; Waters |
Free, Freely available, Registration required for some sites | nlx_152101, biotools:chemspider, r3d100010205 | https://bio.tools/chemspider, https://doi.org/10.17616/R38P4P | SCR_006360 | SciCrunch Registry | 2026-11-07 11:55:53 | 2112 | ||||||
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QCGWAS Resource Report Resource Website 1+ mentions |
QCGWAS (RRID:SCR_006408) | QCGWAS | software resource | Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies. | quality control, genome wide association study, windows, os x, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24395754 | GNU General Public License, v3 or later | OMICS_02203, biotools:qcgwas | https://bio.tools/qcgwas | SCR_006408 | SciCrunch Registry | QCGWAS: Quality Control of Genome Wide Association Study results, Quality Control of Genome Wide Association Study | 2026-11-07 11:55:54 | 7 | |||||
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SeWeR - SEquence analysis using WEb Resources Resource Report Resource Website |
SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) | data or information resource, portal, service resource, software resource, topical portal | Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C. | nucleic acid, protein, pcr, alignment, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Centre for Cellular and Molecular Biology; Hyderabad; India |
PMID:11395442 | biotools:sewer, nlx_18981 | https://bio.tools/sewer | SCR_004167 | SciCrunch Registry | SEquence analysis using WEb Resources, SeWeR | 2026-11-07 11:55:10 | 0 | |||||||
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PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm, https://sources.debian.org/src/perm/ | SCR_004223 | SciCrunch Registry | PERiodic seed Mapping, Periodic seed Mapping | 2026-11-07 11:55:45 | 60 | ||||||
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TAGS Resource Report Resource Website 100+ mentions |
TAGS (RRID:SCR_004294) | TAGS | data analysis software, data processing software, software application, software resource, time-series analysis software | Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, enrichment analysis, time series, function, structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tags, nlx_31187 | https://bio.tools/tags | http://166.111.130.26/member/yliu/TAGS/ | SCR_004294 | SciCrunch Registry | 2026-11-07 11:55:12 | 139 | ||||||
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BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | data or information resource, data repository, database, service resource, storage service resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | SciCrunch Registry | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-11-07 11:55:18 | 29 | |||||
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STAR Resource Report Resource Website 10000+ mentions |
STAR (RRID:SCR_004463) | alignment software, data processing software, image analysis software, software application, software resource | Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. | RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools |
is used by: STARsolo is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U54 HG004557 | PMID:23104886 DOI:10.1093/bioinformatics/bts635 |
biotools:star, OMICS_01254, SCR_015899 | https://github.com/alexdobin/STAR, https://bio.tools/star, https://sources.debian.org/src/rna-star/ | SCR_004463 | SciCrunch Registry | Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner | 2026-11-07 11:55:21 | 26381 | ||||||
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neurodebian Resource Report Resource Website 10+ mentions |
neurodebian (RRID:SCR_004401) | NeuroDebian | data distribution software, data processing software, software application, software development environment, software development tool, software repository, software resource, source code | Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note. | linux, linux distribution, virtual machine, fmri, eeg, pymvpa, python, r, debian, brain image, neuroscience, platform, afni brik, bshort, bfloat, console (text based), dicom, domain independent, freebsd, gnome, kde, linux, minc2, nifti, philips par/rec, development environment, posix/unix-like, system administrator, web environment |
lists: MRIcron is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP is related to: NITRC Computational Environment is related to: PyMVPA is related to: MRtrix has parent organization: Debian has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany is parent organization of: VoxBo is parent organization of: Computational Morphometry Toolkit |
PMID:23055966 | GNU General Public License v3, The community can contribute to this resource | nlx_143723 | http://www.nitrc.org/projects/neurodebian | SCR_004401 | SciCrunch Registry | Debian Neuroscience Repository, neuro debian | 2026-11-07 11:55:20 | 41 | |||||
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems, https://doi.org/10.17616/R31K80 | SCR_004690 | SciCrunch Registry | BioSystems Database, NCBI BioSystems | 2026-11-07 11:55:34 | 118 | |||||
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QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | controlled vocabulary, data access protocol, data or information resource, database, ontology, software resource, web service | A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. | gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: STRAP has parent organization: European Bioinformatics Institute |
BBSRC BB/E023541/1 | PMID:19744993 PMID:20157483 |
Apache License, v2, Free for academic use | biotools:quickgo, nlx_60318, OMICS_02276 | https://bio.tools/quickgo | SCR_004608 | SciCrunch Registry | Quick GO | 2026-11-07 11:55:23 | 556 | ||||
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BioPig Resource Report Resource Website 1+ mentions |
BioPig (RRID:SCR_004636) | BioPig | software resource | Software providing a framework for genomic data analysis using Apache Pig and Hadoop. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
PMID:24021384 | biotools:biopig, OMICS_01225 | https://bio.tools/biopig | SCR_004636 | SciCrunch Registry | 2026-11-07 11:55:33 | 2 | |||||||
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Small Molecule Pathway Database Resource Report Resource Website 100+ mentions |
Small Molecule Pathway Database (RRID:SCR_004844) | SMPDB | analysis service resource, data analysis service, data or information resource, database, image, production service resource, service resource | An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable. | metabolomics, transcriptomics, proteomics, systems biology, small molecule, pathway, human, metabolic pathway, metabolic disease pathway, metabolite signaling pathway, drug-action pathway, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ConsensusPathDB has parent organization: University of Alberta; Alberta; Canada |
Genome Alberta ; Genome Canada |
PMID:19948758 | nlx_143926, biotools:smpdb, r3d100012753 | https://bio.tools/smpdb, https://doi.org/10.17616/R3TB93 | SCR_004844 | SciCrunch Registry | SMPDB (The Small Molecule Pathway Database), Small Molecule Pathway Database (SMPDB) | 2026-11-07 11:55:50 | 120 | |||||
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ANTS - Advanced Normalization ToolS Resource Report Resource Website 500+ mentions |
ANTS - Advanced Normalization ToolS (RRID:SCR_004757) | ANTS, ANTsX | data processing software, image analysis software, registration software, segmentation software, software application, software resource | Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion. | algorithm, atlas application, morphology, segmentation, image registration, temporal transformation, child, pediatric, normalization |
is used by: CMIND PY is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Segmentation of Hippocampus Subfields is related to: ANTsR has parent organization: University of Pennsylvania; Philadelphia; USA |
NIBIB R01 EB006266 | PMID:20851191 PMID:33907199 |
nlx_75959 | http://www.nitrc.org/projects/ants, https://sources.debian.org/src/ants/, https://gist.github.com/ntustison/12a656a5fc2f6f9c4494c88dc09c5621 | SCR_004757 | SciCrunch Registry | Advanced Normalization Tools | 2026-11-07 11:55:19 | 525 | |||||
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NCBI Probe Resource Report Resource Website 10+ mentions |
NCBI Probe (RRID:SCR_004816) | NCBI Probe | data or information resource, data repository, database, service resource, storage service resource | Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database. | reagent, probe, registry, nucleic acid, gene expression, gene mapping, gene silencing, dna data bank, nucleic acid probe, gold standard, bio.tools |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: UniSTS has parent organization: NCBI |
Public, The community can contribute to this resource | nlx_80513, r3d100010780, biotools:ncbi_dbprobe | http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe, https://bio.tools/ncbi_dbprobe, https://doi.org/10.17616/R3D041 | SCR_004816 | SciCrunch Registry | NCBI Probe Database, Entrez Probe Database, ProbeDB, Probe Database, dbProbe | 2026-11-07 11:55:26 | 17 |
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