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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | web service, software resource, application programming interface, data access protocol, data or information resource | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-08-04 09:44:20 | 2 | |||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data processing software, data analysis software, software resource, software application, data visualization software | Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. | Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization | NSF IIS 1251151 | Free, Available for download, Freely available | SCR_018511 | 2026-08-04 09:44:21 | 10 | ||||||||||
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Vital Signs Ontology Resource Report Resource Website 1+ mentions |
Vital Signs Ontology (RRID:SCR_001422) | VSO | ontology, data or information resource, controlled vocabulary | Ontology for the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. It provides a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. | ontology, controlled vocabulary, vital signs, data, measurement, blood pressure, body temperature, respiration rate, pulse rate | is used by: TRANSFoRm Clinical Data Integration Model | nif-0000-02605 | https://bioportal.bioontology.org/ontologies/VSO | http://code.google.com/p/vital-signs-ontology/ | SCR_001422 | vital-signs-ontology | 2026-08-04 09:40:23 | 1 | ||||||
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National Center for Integrative Biomedical Informatics Resource Report Resource Website 1+ mentions |
National Center for Integrative Biomedical Informatics (RRID:SCR_001538) | portal, organization portal, data or information resource | The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519. | analysis tools, bipolar disorder, code, computational infrastructure, conceptual models, data, diabetes, knowledge repository, presentations, prostate cancer, query tools, seminar material, tool development, tutorials, videos, model |
is listed by: 3DVC is related to: Biological Concept Diagram Editor is related to: Gene Interaction Extraction from the Literature is related to: National Centers for Biomedical Computing has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Substructure Index-based Approximate Graph Alignment is parent organization of: miniTUBA is parent organization of: Michigan Molecular Interactions is parent organization of: Cell Line Knowledge Base is parent organization of: HubMed is parent organization of: MiMI Plugin for Cytoscape |
Type 1 diabetes, Type 2 diabetes, Diabetes, Cancer, Bipolar disorder | PMID:22101971 | Free, Freely available | nif-0000-09660 | http://portal.ncibi.org/gateway/ | SCR_001538 | NCIBI | 2026-08-04 09:40:24 | 1 | |||||
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Farsight Toolkit Resource Report Resource Website 1+ mentions |
Farsight Toolkit (RRID:SCR_001728) | FARSIGHT | data processing software, software resource, software application, image processing software, image analysis software, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules. | editing, 2d, 3d, algorithm, analysis, bio-format, computational, data, graphical, inspection, metadata, microscopy, morphological, morphology, pixel, processing, segmentation, taxonomy, image | has parent organization: University of Houston; Texas; USA | NIBIB R01-EB005157; NSF EEC-9986821; NIBIB R01EB005157 |
PMID:24808857 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10227 | SCR_001728 | FARSIGHTWiki | 2026-08-04 09:40:27 | 2 | |||||
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FreeSurfer Resource Report Resource Website 10000+ mentions |
FreeSurfer (RRID:SCR_001847) | FreeSurfer | data processing software, software resource, software application, image analysis software, data visualization software | Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. | processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data |
is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox is used by: freesurfR is used by: Automatic Analysis is used by: NHP Freesurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian is listed by: SoftCite is related to: PySurfer is related to: RFT FDR is related to: FMRLAB is related to: TRACULA is related to: BASH4RfMRI has parent organization: Harvard University; Cambridge; United States has plug in: JOSA works with: NIAG Addiction Data |
NCRR U24 RR021382; NINDS R01 NS052585; NCRR RR014075 |
PMID:22248573 | Free, Available for download, Freely available | nif-0000-00304 | https://sources.debian.org/src/freesurfer/, http://www.nitrc.org/projects/freesurfer, http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall | SCR_001847 | 2026-08-04 09:40:29 | 11817 | |||||
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Dataverse Network Project Resource Report Resource Website 10+ mentions |
Dataverse Network Project (RRID:SCR_001997) | Dataverse | portal, database, storage service resource, data repository, service resource, project portal, catalog, data or information resource | Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization. | data, repository, collection, publishing, citing, sharing, discovering, research, community, connection |
is used by: UCSF DataShare is used by: Agri-environmental Research Data Repository is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is related to: PROMIS 2 MY Health has parent organization: Harvard University; Cambridge; United States is parent organization of: Universal Numerical Fingerprint is parent organization of: Agri-environmental Research Data Repository |
Alfred P. Sloan Foundation ; NSF ; Microsoft Research |
Free, Available for download, Freely available | r3d100010051, nif-0000-00316 | https://doi.org/10.17616/R3C880 | http://thedata.org/ | SCR_001997 | Harvard Dataverse, The Dataverse Project, Dataverse, Dataverse Network, Dataverse Network Project, Dataverse Project | 2026-08-04 09:40:31 | 12 | ||||
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SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
Wellcome Trust ; NHGRI U54 HG002750 |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools, https://github.com/samtools/htslib, https://bio.tools/samtools, https://sources.debian.org/src/samtools/ | http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-08-04 09:40:33 | 30156 | |||
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AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium. | search, sort, analyze, visualize, data, ontology, gene, annotation, FASEB list |
uses: GOlr is used by: NIF Data Federation is listed by: OMICtools is listed by: Gene Ontology Tools is related to: ASAP is related to: Candida Genome Database is related to: Berkeley Bioinformatics Open-Source Projects is related to: ECO is related to: Zebrafish Information Network (ZFIN) is related to: Gramene is related to: WormBase is related to: NCBI Protein Database is related to: UniProtKB is related to: GeneDB Lmajor is related to: TAIR is related to: SGD is related to: GeneDB Tbrucei is related to: VMD is related to: JCVI CMR is related to: go-db-perl is related to: Mouse Genome Informatics (MGI) is related to: NCBI is related to: FlyBase is related to: GeneDB Pfalciparum is related to: PomBase is related to: Pseudomonas Genome Database is related to: Dictyostelium discoideum genome database is related to: Plant Ontology is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: MeGO is related to: ASPGD is related to: EcoCyc is related to: Reactome is related to: SGN is related to: GO-Module is related to: Songbird Brain Transcriptome Database is related to: Rat Genome Database (RGD) is related to: RamiGO has parent organization: Gene Ontology |
NHGRI P41 HG002273 | PMID:19033274 | Free, Available for download, Freely available | nif-0000-20935, OMICS_02266 | http://sourceforge.net/projects/geneontology/ | SCR_002143 | GO Consortium, AmiGO, AmiGO 2, AmiGene Ontology, Gene Ontology Database, Gene Ontology Consortium, GO Database, The Gene Ontology Consortium | 2026-08-04 09:40:34 | 1242 | ||||
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NITRC Enhanced Services Resource Report Resource Website |
NITRC Enhanced Services (RRID:SCR_002494) | NITRC Enhanced Services | portal, community building portal, data or information resource, service resource | Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data. | data, database, data resource, dicom, domain independent, information resource, nifti, platform or development environment, software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NITRC Computational Environment is related to: NITRC-IR has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155890 | SCR_002494 | 2026-08-04 09:40:39 | 0 | ||||||||
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RSEM Resource Report Resource Website 50+ mentions |
RSEM (RRID:SCR_000262) | data processing software, software application, software resource, data analysis software | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-08-04 09:40:05 | 94 | ||||||
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UNAVCO Geodetic Web Services Resource Report Resource Website |
UNAVCO Geodetic Web Services (RRID:SCR_000181) | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description. | geodesy, geophysics, gps, pore, tilt, strain, json, met, data |
is listed by: CINERGI has parent organization: UNAVCO |
THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000177 | SCR_000181 | 2026-08-04 09:40:04 | 0 | |||||||||
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Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility Resource Report Resource Website |
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) | analysis service resource, access service resource, core facility, production service resource, service resource | Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations. | affymetrix, array, PCPGM, gene, expression, data, analysis, service |
is listed by: Eagle I has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156324 | http://www.partners.org/researchcores/trash/bioinformatics_HPCGG.html | SCR_000882 | PCPGM, bioinformatics, The Partners HealthCare Center for Personalized Genetic Medicine | 2026-08-04 09:40:15 | 0 | |||||||
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Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | data processing software, data analysis software, software resource, sequence analysis software, software application | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | 2026-08-04 09:40:18 | 0 | |||||||||
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Waxholm Space Resource Report Resource Website 10+ mentions |
Waxholm Space (RRID:SCR_001592) | WHS, WSA, WSS | data or information resource, narrative resource, standard specification, atlas, waxholm atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files. | mouse WHS atlas, neuroanatomy, mapping, atlas, digital, brain, reference, registration, neuroanatomical, data, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Waxholm Space is related to: Duke University; North Carolina; USA is related to: PMOD Software is related to: ITK-SNAP has parent organization: International Neuroinformatics Coordinating Facility has parent organization: University of Oslo; Oslo; Norway works with: MeshView works with: VisuAlign |
PMID:20600960 PMID:21304938 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_009594, nlx_153838, nlx_155839 | http://software.incf.org/software/waxholm-space/home, http://www.nitrc.org/projects/incf_waxholm-sp | SCR_001592 | Waxholm Space Atlas, Waxholm Space, Waxholm Standard Space, Mouse WHS atlas | 2026-08-04 09:40:25 | 16 | |||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | portal, project portal, service resource, database, data or information resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase works with: bedGraphToBigWig |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu, https://doi.org/10.17616/R3RK5C | SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-08-04 09:41:26 | 10026 | ||||||
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Digital Access to Scholarship at Harvard Resource Report Resource Website |
Digital Access to Scholarship at Harvard (RRID:SCR_004122) | DASH | storage service resource, data repository, service resource, database, data or information resource | Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH. | scholarship, image, audio clip, video resource, manuscript, data | has parent organization: Harvard University; Cambridge; United States | nlx_158606 | SCR_004122 | 2026-08-04 09:41:03 | 0 | |||||||||
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OpenNeuro Resource Report Resource Website 100+ mentions |
OpenNeuro (RRID:SCR_005031) | OpenNeuro, OpenfMRI | image repository, storage service resource, data repository, service resource, database, data or information resource | Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. | neuroinformatics, database, storing, dataset, neuroimaging, data, MRI, MEG, EEG, iEEG, ECoG, FASEB list |
uses: Brain Imaging Data Structure (BIDs) uses: HED Tags is used by: studyforrest.org is used by: DataLad is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is used by: Baby Open Brains is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing is affiliated with: NEMAR is related to: Integrated Manually Extracted Annotation has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Reproducible Neuroscience has parent organization: BRAIN Initiative is provided by: OpenNeuro |
NSF OCI1131441; NIDA ; Laura and John Arnold Foundation ; Stanford ; Squishymedia ; BRAIN Initiative ; NIMH |
Free, Freely available | DOI:10.25504/FAIRsharing.s1r9bw, r3d100010924, nlx_144048, DOI:10.17616/R33047, DOI:10.18112 | http://www.nitrc.org/projects/openfmri, https://github.com/OpenNeuroDatasets, https://doi.org/10.17616/R33047, https://doi.org/10.17616/r33047, https://doi.org/10.18112/, https://dx.doi.org/10.18112/, https://fairsharing.org/10.25504/FAIRsharing.s1r9bw, https://doi.org/10.17616/R33047 | http://openfmri.org | SCR_005031 | OpenfMRI, Open fMRI, OpenNeuro | 2026-08-04 09:41:17 | 247 | ||||
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Neuroscience Gateway Resource Report Resource Website 10+ mentions |
Neuroscience Gateway (RRID:SCR_008915) | NSG | portal, software resource, project portal, data or information resource | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative |
is recommended by: BRAIN Initiative lists: ModelRun is related to: XSEDE - Extreme Science and Engineering Discovery Environment is related to: NEURON is related to: GENESIS Neural Database and Modelers Workspace has parent organization: San Diego Supercomputer Center has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NSF 1458840; NSF 1458495; BBSRC N005236; NIBIB R01 EB023297; NSF 1339856; NSF 1146949 |
Free, Freely available | nlx_151553, SCR_015767 | http://www.nitrc.org/projects/nsg/ | SCR_008915 | Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal | 2026-08-04 09:42:14 | 23 | |||||
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Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | data processing software, software application, software resource | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore, https://bio.tools/trim_galore, https://sources.debian.org/src/trim-galore/ | SCR_011847 | TrimGalore | 2026-08-04 09:42:52 | 6255 |
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