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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GRS Resource Report Resource Website 1+ mentions |
GRS (RRID:SCR_001008) | data analysis software, data processing software, data management software, software application, software resource | A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence. | data analysis software, data management software, compression tool, data compression, storage, genome, resequencing | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00960 | SCR_001008 | 2026-08-09 09:03:05 | 2 | |||||||||
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FACTA+. Resource Report Resource Website 1+ mentions |
FACTA+. (RRID:SCR_001767) | FACTA+ | web service, service resource, software resource, data access protocol | Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/ | text mining, gene, protein, disease, symptom, drug, enzyme, compound, biomedical, association, machine learning, chemical, text-mining software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:18772154 | Free, Freely available | biotools:facta_plus, nif-0000-10272, OMICS_01181 | http://refine1-nactem.mc.man.ac.uk/facta/, https://bio.tools/facta_plus | SCR_001767 | Finding Associated Concepts with Text Analysis | 2026-08-09 09:03:16 | 2 | ||||
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NTAP Resource Report Resource Website 10+ mentions |
NTAP (RRID:SCR_001488) | NTAP | data analysis software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl. | software, tiling array, data analysis, rice, arabidopsis, hy5, transcription factor, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:19468055 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00808 | SCR_001488 | NimbleGen Tiling array Analysis Package, NimbleGen Tilingarray Analysis Package | 2026-08-09 09:03:11 | 10 | ||||||
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ImaGene Resource Report Resource Website 100+ mentions |
ImaGene (RRID:SCR_002178) | data analysis software, software resource, software application, data processing software | Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microarray analysis, machine vision, convolutional neural network, quantify natural selection, genomic data, population genomic data, evolutionary population, genetics model, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Imperial College London ; Politecnico di Milano |
PMID:31757205 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ImaGene, OMICS_00841 | https://github.com/mfumagalli/ImaGene, https://bio.tools/ImaGene | http://www.biodiscovery.com/software/imagene/ | SCR_002178 | 2026-08-09 09:03:22 | 405 | |||||
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TumorSim Resource Report Resource Website 1+ mentions |
TumorSim (RRID:SCR_002604) | simulation software, software application, software resource | Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images. | clinical neuroinformatics, magnetic resonance, mri, brain, segmentation, simulation, tumor, ground truth |
uses: BrainWeb - Simulated Brain Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
Cancer | NIBIB R01 EB000219 | PMID:19119055 | Free, Available for download, Freely available | nlx_156007 | SCR_002604 | 2026-08-09 09:03:32 | 1 | ||||||
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Open Source Brain Resource Report Resource Website 10+ mentions |
Open Source Brain (RRID:SCR_001393) | OSB | database, data or information resource, service resource, storage service resource, data repository | A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome. | model, neuroml, pynn, computational model, neural system, neuron, disease, data analysis service, visualization, 3d explorer, network, ion channel distribution, ion channel, microcircuit |
uses: PyNN uses: NeuroML is used by: NIF Data Federation is listed by: Integrated Models is related to: neuroConstruct is related to: NWB Explorer is related to: Allen Institute for Brain Science has parent organization: University College London; London; United Kingdom |
Wellcome Trust | Free, Freely Available | nlx_152590 | SCR_001393 | OpenSourceBrain | 2026-08-09 09:03:09 | 27 | ||||||
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SNPMeta Resource Report Resource Website 1+ mentions |
SNPMeta (RRID:SCR_002005) | SNPMeta | service resource, data analysis service, analysis service resource, software resource, production service resource | A Python and BioPython-based tool to generate metadata for single nucleotide polymorphisms (SNPs) for easy filtering, or submission to SNP databases. Information reported includes gene name, whether the SNP is coding or noncoding, and whether the SNP is synonymous or nonsynonymous. SNPMeta outputs in either a dbSNP submission report format, or a tab-delimited format. There is a also Web-based version available that only annotates with default settings, and only annotates a maximum of 20 SNPs at one time. The script may be downloaded for full functionality. | single nucleotide polymorphism, coding, noncoding, , synonymous, nonsynonymous, python, biopython, metadata, annotation |
is listed by: OMICtools has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:24237904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01923 | SCR_002005 | 2026-08-09 09:03:21 | 1 | |||||||
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FusionCatcher Resource Report Resource Website 1+ mentions |
FusionCatcher (RRID:SCR_000060) | data analysis software, data processing software, software application, sequence analysis software, software resource | Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. | fusion gene, known fusion gene, translocation, chimera, rna-seq data, hiseq, solexa, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/011650 | Free, Available for download, Freely available | biotools:fusioncatcher, OMICS_01348 | https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md, https://bio.tools/fusioncatcher | http://code.google.com/p/fusioncatcher/ | SCR_000060 | 2026-08-09 09:02:54 | 9 | ||||||
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ChemChaste Resource Report Resource Website 1+ mentions |
ChemChaste (RRID:SCR_022208) | simulation software, software application, software resource | Software tool for simulating spatially inhomogenous biochemical reaction diffusion systems for modelling cell environment feedbacks. Simulation software for spatially organised biochemical systems. | spatially organised, biochemical systems, simulating biochemical systems, spatially inhomogenous biochemical reaction diffusion systems, modelling cell environment feedbacks | DOI:10.1101/2021.10.21.465304 | Free, Available for download, Freely available | SCR_022208 | 2026-08-09 09:08:12 | 1 | ||||||||||
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Spacemake Resource Report Resource Website 1+ mentions |
Spacemake (RRID:SCR_022207) | data analysis software, software resource, software application, data processing software | Software pipeline for processing and analysis of large scale spatial transcriptomics data. Enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports. | spatial dataset, gene counts, large scale spatial transcriptomics data, transcriptomics data, spatial transcriptomics data, raw sequencing data, analysis reports | DOI:10.1101/2021.11.07.467598 | Free, Available for download, Freely available | SCR_022207 | spacemake | 2026-08-09 09:07:50 | 2 | |||||||||
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QualitySNPng Resource Report Resource Website 1+ mentions |
QualitySNPng (RRID:SCR_002479) | standalone software, data processing software, software application, data visualization software, software resource | Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy. | single nucleotide polymorphism, haplotype strategy, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23632165 | Free, Available for download, Freely available | biotools:qualitysnpng, OMICS_00070 | https://bio.tools/qualitysnpng | SCR_002479 | 2026-08-09 09:03:29 | 7 | |||||||
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PBSIM Resource Report Resource Website 10+ mentions |
PBSIM (RRID:SCR_002512) | simulation software, software application, software resource | Software that simulates PacBio reads by using either a model-based or sampling-based simulation. | pacbio simulation, model-based simulation, sampling-based simulation |
is listed by: OMICtools is listed by: Debian |
PMID:23129296 DOI:10.1093/bioinformatics/bts649 |
Free, Available for download, Freely available | OMICS_00253 | https://sources.debian.org/src/pbsim/ | SCR_002512 | PacBio reads simulator | 2026-08-09 09:03:27 | 11 | ||||||
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MAQC Resource Report Resource Website 10+ mentions |
MAQC (RRID:SCR_002351) | MAQC | knowledge environment, data or information resource, standard specification, narrative resource | Project to improve the microarray and next-generation sequencing technologies and foster their proper applications in discovery, development and review of FDA regulated products by developing standards and quality measures. Microarrays and next-generation sequencing represent core technologies in pharmacogenomics and toxicogenomics; however, before these technologies can successfully and reliably be used in clinical practice and regulatory decision-making, standards and quality measures need to be developed. Everyone is invited to participate in the MAQC project. | microarray, next-generation sequencing, pharmacogenomics, toxicogenomics, quality control |
is listed by: OMICtools has parent organization: National Center for Toxicological Research |
OMICS_01784 | SCR_002351 | MicroArray Quality Control | 2026-08-09 09:03:24 | 21 | ||||||||
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SpineSegmentation module for 3DSlicer Resource Report Resource Website 1+ mentions |
SpineSegmentation module for 3DSlicer (RRID:SCR_002593) | Spine Segmentation Module in Slicer3 | data processing software, software application, image analysis software, segmentation software, software resource | 3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010. | magnetic resonance, spine |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: National Alliance for Medical Image Computing |
Free, Freely available | nlx_155997 | http://www.nitrc.org/projects/sylvainproject | SCR_002593 | Spine Segmentation module for 3D Slicer | 2026-08-09 09:03:36 | 3 | ||||||
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GitHub Resource Report Resource Website 1000+ mentions |
GitHub (RRID:SCR_002630) | GitHub | service resource, mobile app, software repository, software application, commercial organization, software resource | A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go. | source code, database, java, php, python, objective-c, c++, c, c#, perl, issue, computer science, FASEB list |
is used by: Observational Medical Outcomes Partnership is used by: NIH Heal Project lists: Digital Asset Management System lists: IBMA toolbox lists: NeuroSynth lists: MIAPA lists: FACS lists: RSEM lists: flowPeaks lists: BRAINSCut lists: Mspire-Simulator is listed by: FORCE11 is listed by: re3data.org is related to: Karma is related to: ImpactStory hosts: SciUnit hosts: FlashX hosts: BioBlend Library hosts: Vision Egg hosts: Cufflinks hosts: MetAMOS hosts: ProtVista hosts: Big Data Bag hosts: FUSIM hosts: GDC hosts: ProtTest hosts: State Space Models hosts: OpenWorm hosts: Zero Mode Waveguide Imaging and Analysis package tools hosts: Taxonomer hosts: Eelbrain hosts: N2A hosts: Pilon hosts: MicroDraw hosts: BrainBox hosts: Stanford CoreNLP hosts: AnaMorph hosts: wMICA hosts: SEER hosts: phytools hosts: PhenVar hosts: JuncBASE hosts: HISAT2 hosts: NeuroManager |
Free, Available for download, Freely available | nlx_156051 | http://www.force11.org/node/4710 | SCR_002630 | 2026-08-09 09:03:33 | 3749 | |||||||
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RAVEN Resource Report Resource Website 100+ mentions |
RAVEN (RRID:SCR_001937) | RAVEN | database, data or information resource, service resource, data analysis service, analysis service resource, production service resource | Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor binding site, phylogenetic footprint, regulatory sequence variation, genetic variation, in silico, regulatory sequence, FASEB list |
uses: Embassy-domsearch is listed by: OMICtools has parent organization: University of British Columbia; British Columbia; Canada |
PMID:18208319 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01932 | SCR_001937 | Regulatory analysis of Variation in Enhancers, RAVEN - Regulatory analysis of Variation in ENhancers | 2026-08-09 09:03:20 | 127 | ||||||
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Nitime Resource Report Resource Website 10+ mentions |
Nitime (RRID:SCR_002504) | NiTime | data analysis software, software library, data processing software, software application, software toolkit, software resource | Software library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code. | eeg, meg, electrocorticography, magnetic resonance, time-series, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
Free, Available for download, Freely available | nlx_155903 | http://www.nitrc.org/projects/nitime | SCR_002504 | Nitime: time-series analysis for neuroscience | 2026-08-09 09:03:35 | 23 | ||||||
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Neurolucida Resource Report Resource Website 1000+ mentions |
Neurolucida (RRID:SCR_001775) | data analysis software, data processing software, software application, data visualization software, software resource | Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience. | electron microscope, fluorescent, 3d mapping, anatomical, brian, brightfield, camera, confocal, digital, hardware, mapping, microscope, morphometry, neuron, reconstruction, scanning tomographic, software, tissue, virtual, video, image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:2224829 | Restricted | nif-0000-10294 | http://www.nitrc.org/projects/neurolucida | http://www.mbfbioscience.com/neurolucida/neurolucida | SCR_001775 | MBF Neurolucida | 2026-08-09 09:03:16 | 3396 | |||||
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VIRsiRNAdb Resource Report Resource Website 1+ mentions |
VIRsiRNAdb (RRID:SCR_006108) | VIRsiRNAdb | database, data or information resource, service resource, storage service resource, data repository, data analysis service, analysis service resource, production service resource | VIRsiRNAdb is a curated database of experimentally validated viral siRNA / shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Submissions are welcome. Currently, the database provides detailed experimental information of 1358 siRNA/shRNA which includes siRNA sequence, virus subtype, target gene, GenBank accession, design algorithm, cell type, test object, test method and efficacy (mostly quantitative efficacies). Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. The database has facilities like search, advance search (using Boolean operators AND, OR) browsing (with data sorting option), internal linking and external linking to other databases (Pubmed, Genbank, ICTV). Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences. virsiRNAdb would prove useful for RNAi researchers especially in siRNA based antiviral therapeutics development. | virus, sirna, shrna, gene, influenza, sars, hepatitis, sirna sequence, virus subtype, target gene, genbank accession, design algorithm, cell type, efficacy, target genome region, target object, experimental assay, off-target, sirna matching, reference viral sequence, influenza virus, hepatitis b virus, hpv, sars corona virus, viral genome, reference genome, align, sirna sequence, fasta, blast, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
Influenza, SARS, Hepatitis, Infectious disease | Council of Scientific and Industrial Research; New Delhi; India | PMID:22139916 | Open unspecified license / Freely available | nlx_151610, biotools:virsirnadb | https://bio.tools/virsirnadb | SCR_006108 | VIRsiRNAdb - Database of Viral siRNA / shRNA, Viral siRNA Database, Viral siRNA Database (VIRsiRNAdb) | 2026-08-09 09:04:21 | 4 | |||
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Gene Expression Omnibus (GEO) Resource Report Resource Website 10000+ mentions |
Gene Expression Omnibus (GEO) (RRID:SCR_005012) | GEO | database, data or information resource, service resource, storage service resource, data repository | Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries. | gold standard, genomics, data, repository, microarray, mRNA, DNA, protein, analysis, SAGE, mass spectrometry, dataset |
is used by: ChIPseeker is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Allen Institute for Brain Science has parent organization: NCBI works with: shinyGEO works with: Drug Gene Budger works with: Signaling Pathways Project works with: GEN3VA |
National Library of Medicine | PMID:23193258 PMID:21097893 PMID:18940857 PMID:17160034 PMID:17099226 PMID:16939800 PMID:16888359 PMID:15608262 PMID:11752295 |
r3d100010283, nif-0000-00142, nlx_96903, OMICS_01030, SCR_007303 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds, http://www.ncbi.nlm.nih.gov/geo/, https://doi.org/10.17616/R33P44 | http://www.ncbi.nlm.nih.gov/gds | SCR_005012 | Gene Expression Omnibus (GEO), Entrez GEO DataSets, Gene Expression Data Sets, Gene Expression Omnibus, GEO, NCBI GEO DataSets, GEO DataSets, Gene Expression Omnibus DataSets | 2026-08-09 09:04:11 | 14348 |
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