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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GeneChip Operating Software Resource Report Resource Website 500+ mentions |
GeneChip Operating Software (RRID:SCR_003408) | GCOS | data analysis software, data processing software, sequence analysis software, software application, software resource | Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request. | gene expression, snp mapping, resequencing, analysis, genotyping, platform, software, comparison, analysis |
is listed by: Biositemaps is listed by: SoftCite has parent organization: Scripps Research Institute |
Free, Available for download, Freely available | nif-0000-33019 | https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/genechip-operating-software-service-pack-2-software-update.html | SCR_003408 | GeneChip Operating Software (GCOS), DNA Array Core Facility GeneChip Operating Software, DNA Array Core Facility GeneChip Operating Software (GCOS) | 2026-09-12 12:55:57 | 650 | ||||||
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Weighted Gene Co-expression Network Analysis Resource Report Resource Website 1000+ mentions |
Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) | WGCNA | data analysis software, data processing software, software application, software resource | Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, co-expression, analysis, network, bio.tools, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
NCI P50CA092131; NIDA 1R01DA030913-01; NIDCR R01DE019255; NIAID U19 AI063603-01 |
PMID:19114008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31889, biotools:crosslinkwgcna | http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation, https://bio.tools/crosslinkwgcna | SCR_003302 | WGCNA: an R package for weighted correlation network analysis | 2026-09-12 12:55:55 | 1879 | ||||
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Software Distribution Sets Resource Report Resource Website |
Software Distribution Sets (RRID:SCR_003465) | Software Distribution Sets | data analysis software, data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. These distribution sets contain software modules and/or data sets extracted from the Visualization and Analysis Software Tools (VAST) library developed at the Minneapolis VA Medical Center, the University of Minnesota and/or the International Consortium for Neuroimaging (INC) (partially funded by the Human Brain Project ) | analysis, module, software, visualization, neuroimaging, data set, functional, statistical |
is listed by: 3DVC is related to: Biositemaps has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
Human Brain Project | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33396 | http://neurovia.umn.edu/incweb/download_home.html | SCR_003465 | 2026-09-12 12:55:58 | 0 | ||||||
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Elephant Resource Report Resource Website 10+ mentions |
Elephant (RRID:SCR_003833) | Elephant, ElePhAnT | data analysis software, data processing software, software application, software resource, software toolkit | The Electrophysiology Analysis Toolkit (Elephant) is a Python library that provides a modular framework for the analysis of experimental and simulated neuronal activity data, such as spike trains, local field potentials, and intracellular data. Elephant builds on the Neo data model to facilitate usability, to enable interoperability, and to support data from dozens of file formats and network simulation tools. Its analysis functions are continuously validated against reference implementations and reports in the literature. Visualizations of analysis results are made available via the Viziphant companion library. Elephant aims to act as a platform for sharing analysis methods across the field. | electrophysiology, analysis, spike train, local field potential, python |
uses: Neo uses: NumPy uses: SciPy is used by: NetworkUnit has parent organization: NeuralEnsemble |
PMID:31449837 | Free, Available for download, Freely available | nlx_158148 | https://github.com/NeuralEnsemble/elephant | SCR_003833 | Elephant - Electrophysiology Analysis Toolkit, Electrophysiology Analysis Toolkit | 2026-09-12 12:56:03 | 30 | |||||
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FieldTrip Resource Report Resource Website 1000+ mentions |
FieldTrip (RRID:SCR_004849) | data analysis software, data processing software, software application, software resource, software toolkit | Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists. | MEG, EEG, iEEG, analysis, data, time, frequency, source, reconstruction, dipole, beamformers, non parametric, statistical, testing |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Connectome Coordination Facility has parent organization: Radboud University; Nijmegen; The Netherlands works with: CoSMoMVPA works with: SleepTrip works with: EEGLAB works with: SPM |
Human Connectome project ; Netherlands Ministry of Economic Affairs ; Netherlands Ministry of Education Culture and Science ; NIH Blueprint for Neuroscience Research |
PMID:21253357 | Free, Available for download, Freely available, Tutorial available | nlx_143928 | http://www.nitrc.org/projects/fieldtrip | SCR_004849 | 2026-09-12 12:56:17 | 3297 | ||||||
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CHAoS Resource Report Resource Website 10+ mentions |
CHAoS (RRID:SCR_005174) | CHAoS | software resource | A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization. | annotation, analysis, visualization, variant, high-throughput sequencing, perl, population genetic, transcript, positional record, sequence, motif, genotype |
is listed by: OMICtools has parent organization: Wellcome Trust Centre for Human Genetics |
GNU General Public License, v2 | OMICS_00170 | SCR_005174 | chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments | 2026-09-12 12:56:22 | 29 | |||||||
|
HIVCD Resource Report Resource Website |
HIVCD (RRID:SCR_005201) | HIVCD | software resource | Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. | java, perl, contamination, sequencing, error, pairwise comparison, testing, analysis, contamination screening |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23583427 | Apache License, v2 | OMICS_00220 | SCR_005201 | HIVCD - Informatics tool for contamination screening in the HIV sequencing lab, HIV Contamination Detection | 2026-09-12 12:56:22 | 0 | ||||||
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Neuromorphometrics Resource Report Resource Website 100+ mentions |
Neuromorphometrics (RRID:SCR_005656) | Neuromorphometrics Inc. | data or information resource, organization portal, portal, service resource, software resource, web application | Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas. | brain, human, modeling, measurement, quantitative, volume, shape, location, neuroanatomical, structure, MRI, scan, analysis, database, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainColor: Collaborative Open Labeling Online Resource is related to: 2012 MICCAI Multi-Atlas Labeling Challenge Data is parent organization of: NVM is parent organization of: Manually Labeled MRI Brain Scan Database is parent organization of: MRI Neuroanatomy Labeling Services |
NIMH R43 MH084358 | Free Demo available for download, Commercially available, Discount for academic use available | SCR_014141, nlx_149079 | http://www.nitrc.org/projects/brain_labeling | SCR_005656 | MRI Brain Anatomy Labeling Services, Quantitative Measurements in MR Brain Images | 2026-09-12 12:56:29 | 428 | |||||
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Onto-Express Resource Report Resource Website 50+ mentions |
Onto-Express (RRID:SCR_005670) | OE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool | microarray, gene, ontology, gene expression, biochemical function, biological process, cellular role, cellular component, molecular function, chromosome location, java, data-mining, browser, visualization, analysis, statistical analysis, term enrichment, search engine, other analysis, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, custom level of abstraction of the gene ontology, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
Wayne State University School of Medicine; Michigan; USA ; NICHD HD36512 |
PMID:12620386 PMID:11829497 PMID:15215428 |
Free for academic use | nlx_149110 | http://vortex.cs.wayne.edu:8080 | SCR_005670 | Onto-Express (OE) | 2026-09-12 12:56:29 | 85 | ||||
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LookSeq Resource Report Resource Website 1+ mentions |
LookSeq (RRID:SCR_005625) | LookSeq | software resource | A web-based application for alignment visualization, browsing and analysis of genome sequence data. | alignment, visualization, browsing, analysis, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00886 | SCR_005625 | 2026-09-12 12:56:29 | 5 | |||||||||
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Northern Ireland Virtual Tissue Archive Resource Report Resource Website |
Northern Ireland Virtual Tissue Archive (RRID:SCR_004452) | NIVTA | data or information resource, image collection, narrative resource, training material | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability. | clinical trial, biomarker research, tissue microarray, analysis, virtual slide, tissue, archive, data resource | has parent organization: Queens University Belfast; Ireland; United Kingdom | Queen's University Belfast; Ireland; United Kingdom ; Hewlett-Packard |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44619 | SCR_004452 | 2026-09-12 12:56:13 | 0 | |||||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | analysis service resource, data or information resource, data repository, database, production service resource, service resource, software resource, source code, storage service resource | An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket. | stem cell, analysis, cancer stem cell, galaxy, gene, pathway, molecular signature, tissue, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard T.H. Chan School of Public Health |
Cancer | NCI 1RC2CA148222-01 | PMID:22121217 | Free, The community can contribute to this resource | biotools:scde_discovery, nlx_44656 | https://bio.tools/scde_discovery | SCR_004453 | Harvard Stem Cell Discovery Engine, SCDE - Stem Cell Discovery Engine | 2026-09-12 12:56:13 | 57 | |||
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Tree and reticulogram REConstruction Resource Report Resource Website 10+ mentions |
Tree and reticulogram REConstruction (RRID:SCR_004497) | T-REX | analysis service resource, data analysis service, production service resource, service resource, software resource | A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. | phylogenetic tree, analysis, visualization, network, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Quebec in Montreal; Quebec; Canada |
PMID:22675075 | biotools:t-rex, OMICS_04264 | https://bio.tools/t-rex | SCR_004497 | Trex-online | 2026-09-12 12:56:13 | 33 | ||||||
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BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | data processing software, data visualization software, image analysis software, software application, software resource | Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction | brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
NIBIB R01 EB002010; NCRR P41 RR013642; NIMH RO1-MH53213 |
PMID:12045000 | nif-0000-30214 | http://www.nitrc.org/projects/brainsuite | SCR_006623 | Brain Suite | 2026-09-12 12:56:42 | 97 | |||||
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InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. | protein, classify, prediction, protein domain, genome, protein family, functional site, protein sequence, protein function, analysis, nucleic acid, amino acid, amino acid sequence, gold standard |
is listed by: re3data.org is listed by: OMICtools is related to: TIGRFAMS is related to: TIGRFAMS is related to: FlyMine is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Biomine is related to: InterProScan is related to: GeneTerm Linker is related to: Gene Ontology is related to: ProDom is related to: Algal Functional Annotation Tool has parent organization: European Bioinformatics Institute |
European Union FP7 Scientific Data Repositories 213037; BBSRC BB/F010508/1; NIGMS GM081084 |
PMID:22096229 PMID:21082426 PMID:18940856 PMID:18428686 PMID:18025686 PMID:17202162 PMID:16909843 PMID:15608177 PMID:12520011 PMID:12230031 PMID:11159333 PMID:11119311 PMID:11125043 |
Acknowledgement requested, Free, Public, The community can contribute to this resource | nif-0000-03035, OMICS_01694, r3d100010798 | https://doi.org/10.17616/R3FS61 | SCR_006695 | InterPro: protein sequence analysis & classification, InterPro protein sequence analysis and classification | 2026-09-12 12:56:43 | 7722 | ||||
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Brain Innovation: Home of the BrainVoyager Product Family Resource Report Resource Website 100+ mentions |
Brain Innovation: Home of the BrainVoyager Product Family (RRID:SCR_006660) | Brain Innovation | data or information resource, portal, software resource, topical portal | Brain Innovation B.V. is developing scientific software in the field of human and animal brain imaging, neural network simulation and computer-based experimental control. Our current major product, BrainVoyager QX, is a commercially available cross-platform neuroimaging tool, which is used in hundreds of labs across the planet. Turbo-BrainVoyager is an easy to use program for real-time data analysis, which allows to observe a subject''s or patient''s brain activity during an ongoing functional MRI scanning session. TMS Neuronavigator provides the hard- and software to navigate a TMS coil to desired anatomical or functionally defined brain regions. We also provide free software products. BrainVoyager Brain Tutor allows to learn about brain areas by clicking on rotatable 3D brain models. StimulDX is a powerful stimulation software based on Microsofts DirectX API, which we will make available for free download in the near future. | brain, imaging, human, non-human animal, brain imaging, neural network simulation, experimental control, network, simulation, experimental, analysis, anatomical, neuroimaging, tool |
is parent organization of: BrainVoyager Brain Tutor is parent organization of: BrainVoyager Brain Viewer is parent organization of: Turbo-BrainVoyager is parent organization of: BrainVoyager |
nif-0000-30213 | SCR_006660 | Brain Innovation B.V. | 2026-09-12 12:56:43 | 174 | ||||||||
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mAdb Resource Report Resource Website 10+ mentions |
mAdb (RRID:SCR_006677) | mAdb | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators. | microarray, bioinformatics, data management, analysis, gene expression, affymetrix, image, alignment, gene array list, cdna, oligonucleotide, gene discovery, prediction, comparison, cancer, FASEB list | has parent organization: Center for Cancer Research | Center for Information Technology | PMID:14728569 | Account required, Restricted to NIH users/collaborators, The community can contribute to this resource | nif-0000-00171 | http://nciarray.nci.nih.gov/ | SCR_006677 | Mad Bee, microArray database, Micro-array Database at the National Cancer Institute, NCI/CIT microArray database | 2026-09-12 12:56:43 | 40 | ||||
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MITK Diffusion Resource Report Resource Website 1+ mentions |
MITK Diffusion (RRID:SCR_006846) | MITK-DI | data processing software, data visualization software, image analysis software, image processing software, software application, software resource, software toolkit, source code | A selection of image analysis algorithms for the processing of diffusion-weighted MR images. Features & Highlights * Tensor and q-ball reconstruction * Glyph visualization * Quantification and partial volume clustering of tensor and q-ball images * Global fiber tractography, visualization, and tract post-processing * Brain network statistics and visualization (connectomics) * Interactive exploration of Tract-based spatial statistics (TBSS) results * Intra-voxel incoherent motion (IVIM) estimation * Synthetic data generation Additional system specific requirements: * Windows: If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2008: 32 bit or 64 bit * Linux: the Qt framework, version 4.6.2 or later Tested systems: Windows 7, Windows Vista; Ubuntu 12.04 and newer; OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion) The OS X 10.6 installer is compatible with OS X 10.7 (Lion) so there is no dedicated disk image build under 10.7. The MITK Diffusion application is based on the MITK research platform and the most of it is open-source. The available code is embedded into the source code of MITK as a module and can be accessed through the public git repository. | tractography, diffusion tensor imaging, q-ball imaging, diffusion mri, data processing, analysis, visualization, connectomics, fiber tractography, tract post processing, glyph visualization, tensor reconstruction, q-ball reconstruction, scalar index, connectivity analysis, image reconstruction, modeling, quantification, segmentation, fiber tracking, macos, windows, os independent, linux, c++, dicom, nifti-1, nrrd, other format |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: German Cancer Research Center |
PMID:23038239 | Most of it, Simplified BSD License | nlx_153917 | http://www.nitrc.org/projects/mitk-diffusion | SCR_006846 | MITK Diffusion Imaging | 2026-09-12 12:56:46 | 3 | |||||
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eXpress Resource Report Resource Website 100+ mentions |
eXpress (RRID:SCR_006873) | eXpress | data analysis software, data processing software, sequence analysis software, software application, software resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018. From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/. Software for streaming quantification for high-throughput DNA/RNA sequencing. Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them. |
quantification, high-throughput, DNA, RNA, sequencing, target, fragment, analysis |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI R01HG006129; NSF |
DOI:10.1038/nmeth.2251 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015990, OMICS_01275 | https://sources.debian.org/src/berkeley-express/ | SCR_006873 | eXpress - Streaming quantification for high-throughput sequencing, Berkeley-express | 2026-09-12 12:56:47 | 495 | ||||
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g:Profiler Resource Report Resource Website 1000+ mentions |
g:Profiler (RRID:SCR_006809) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for functional enrichment analysis and conversions of gene lists. Web based tool for functional profiling of gene lists from large scale experiments. Has web interface with powerful visualization. Used for analyzing data from any organism. | gene, high-throughput, genomics, visualization, statistical analysis, slimmer-type tool, term enrichment, protein interaction, functional similarity, analysis, coexpression, gene id, network enrichment analysis, orthology mapping, genomic locus, ontology or annotation visualization, other analysis, ortholog, functional profile, gene list, ontology, pathway, transcription factor, microrna, regulatory motif, protein-protein interaction, biomolecule, gene expression, gene, homology, single nucleotide polymorphism, dna polymorphism, chromosome, network analysis, disease gene, r |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Ensembl is related to: Ensembl Genomes has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group works with: gProfiler2 |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:21646343 PMID:17478515 PMID:31066453 |
Free, Freely available | OMICS_02223, nif-0000-31975 | SCR_006809 | G:Profiler, g:profiler, gProfiler | 2026-09-12 12:56:46 | 2310 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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