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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser https://bio.tools/rbiopaxparser |
SCR_002744 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-02-14 02:00:19 | 4 | ||||||
|
Gene Ontology Resource Report Resource Website 10000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | knowledge environment resource, portal, consortium, data or information resource, organization portal, project portal | Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases. | gene, product, annotation, molecular, function, cellular, biological, role, database, query, obo, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: GreenPhylDB is used by: LIPID MAPS Proteome Database is used by: Aging Portal is used by: ChannelPedia is used by: Open PHACTS is used by: CoPub is used by: PhenoGO is used by: Database for Annotation Visualization and Integrated Discovery is used by: MitoMiner is used by: dcGO is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: barleyGO is used by: SynGO is used by: Functional Annotation is used by: SwissLipids is listed by: BioPortal is listed by: OBO is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: Mouse Genome Informatics: The Gene Ontology Project is related to: GenNav is related to: SynaptomeDB is related to: High-Throughput GoMiner is related to: Onto-Design is related to: OnEx - Ontology Evolution Explorer is related to: Avadis is related to: GONUTS is related to: PiNGO is related to: Automated Microarray Pipeline is related to: categoryCompare is related to: globaltest is related to: Semantic Measures Library is related to: WegoLoc is related to: AnimalTFDB is related to: MEME Suite - Motif-based sequence analysis tools is related to: Arabidopsis Hormone Database is related to: DAVID is related to: Arabidopsis thaliana Protein Interactome Database is related to: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is related to: pSTIING is related to: GoMiner is related to: FunSimMat is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Centre for Modeling Human Disease Gene Trap Resource is related to: Patterns of Gene Expression in Drosophila Embryogenesis is related to: Babelomics is related to: BioPerl is related to: GeneCruiser is related to: GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool is related to: GOToolBox Functional Investigation of Gene Datasets is related to: Cotton EST Database is related to: MouseNET is related to: PLANTTFDB is related to: T-profiler is related to: Physico-Chemical Process is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: GOCat is related to: Quantitative Enrichment of Sequence Tags is related to: Neural-Immune Gene Ontology is related to: INMEX is related to: StRAnGER is related to: QuickGO is related to: Repository of molecular brain neoplasia data is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PANTHER is related to: Short Time-series Expression Miner (STEM) is related to: DATFAP is related to: GORetriever is related to: Gene Ontology Browsing Utility (GOBU) is related to: GeneTools is related to: GOSlimViewer is related to: go-moose is related to: Network Ontology Analysis is related to: Onto-Compare is related to: Onto-Express is related to: OntoVisT is related to: STRAP is related to: CGAP GO Browser is related to: COBrA is related to: Gene Class Expression is related to: GeneInfoViz is related to: GOfetcher is related to: GoFish is related to: GOProfiler is related to: GOanna is related to: Manatee is related to: Pandora - Protein ANnotation Diagram ORiented Analysis is related to: TAIR Keyword Browser is related to: Wandora is related to: GOTaxExplorer is related to: Onto-Miner is related to: Onto-Translate is related to: ToppGene Suite is related to: DBD - Slim Gene Ontology is related to: ONTO-PERL is related to: Blip: Biomedical Logic Programming is related to: OWL API is related to: CLENCH is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: CateGOrizer is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products is related to: ProteInOn is related to: GeneMerge is related to: GraphWeb is related to: ClueGO is related to: CLASSIFI - Cluster Assignment for Biological Inference is related to: GOHyperGAll is related to: FuncAssociate: The Gene Set Functionator is related to: GOdist is related to: FuncExpression is related to: FunCluster is related to: FIVA - Functional Information Viewer and Analyzer is related to: GARBAN is related to: GOEx - Gene Ontology Explorer is related to: SGD Gene Ontology Slim Mapper is related to: GOArray is related to: SNPsandGO is related to: GoSurfer is related to: GOtcha is related to: MAPPFinder is related to: GoAnnotator is related to: MetaGeneProfiler is related to: OntoGate is related to: ProfCom - Profiling of complex functionality is related to: SerbGO is related to: SOURCE is related to: Ontologizer is related to: THEA - Tools for High-throughput Experiments Analysis is related to: Generic GO Term Mapper is related to: GREAT: Genomic Regions Enrichment of Annotations Tool is related to: GoBean - a Java application for Gene Ontology enrichment analysis is related to: TXTGate is related to: GO-Module is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools is related to: MalaCards is related to: FSST - Functional Similarity Search Tool is related to: Expression Profiler is related to: GOChase is related to: GoPubMed is related to: Whatizit is related to: REViGO is related to: WEGO - Web Gene Ontology Annotation Plot is related to: Blast2GO is related to: InterProScan is related to: PubSearch is related to: TrED is related to: CharProtDB: Characterized Protein Database is related to: VirHostNet: Virus-Host Network is related to: Pathbase is related to: GO Online SQL Environment (GOOSE) is related to: Neurobehavior Ontology is related to: InterSpecies Analysing Application using Containers is related to: KOBAS is related to: ConceptWiki is related to: GeneTerm Linker is related to: Bioconductor is related to: ErmineJ is related to: Gene Ontology For Functional Analysis (GOFFA) is related to: MGI GO Browser is related to: Comparative Toxicogenomics Database (CTD) is related to: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is related to: Ontology Lookup Service is related to: LexGrid is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: g:Profiler is related to: OwlSim is related to: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool is related to: YeTFaSCo is related to: FastSemSim is related to: RamiGO is related to: AutismKB is related to: GeneCodis is related to: FunSpec is related to: FunNet - Transcriptional Networks Analysis is related to: PhenoM - Phenomics of yeast Mutants is related to: agriGO is related to: GOblet is related to: DynGO is related to: SeqExpress is related to: ProbeExplorer is related to: ECgene: Gene Modeling with Alternative Splicing is related to: Organelle DB is related to: Gemma is related to: Candidate Genes to Inherited Diseases is related to: Proteome Analyst PA-GOSUB is related to: Network Analysis, Visualization and Graphing TORonto is related to: GOstat is related to: Onto-Express To Go (OE2GO) is related to: Tk-GO is related to: EGAN: Exploratory Gene Association Networks is related to: Spotfire is related to: GOMO - Gene Ontology for Motifs is related to: GFINDer: Genome Function INtegrated Discoverer is related to: Generic GO Term Finder is related to: Agile Protein Interactomes DataServer is related to: AgingDB is related to: UBERON is related to: Algal Functional Annotation Tool is related to: gsGator is related to: Flash Gviewer is related to: Cerebellar Development Transcriptome Database is related to: PlantNATsDB - Plant Natural Antisense Transcripts DataBase is related to: EASE: the Expression Analysis Systematic Explorer is related to: PiGenome is related to: L2L Microarray Analysis Tool is related to: MeGO is related to: CELDA Ontology is related to: Diabetes Disease Portal is related to: MatrixDB is related to: Kidney and Urinary Pathway Knowledge Base is related to: MouseCyc is related to: Candida Genome Database is related to: Honey Bee Brain EST Project is related to: ECO is related to: FlyMine is related to: Gramene is related to: 3D-Interologs is related to: Biomine is related to: UniProtKB is related to: NCBI BioSystems Database is related to: EBIMed is related to: Coremine Medical is related to: EMAGE Gene Expression Database is related to: GeneMANIA is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: GeneTrail is related to: Magic is related to: Mouse Genome Informatics (MGI) is related to: FlyBase is related to: InterPro is related to: InnateDB is related to: canSAR is related to: HPRD - Human Protein Reference Database is related to: CRCView is related to: Integrated Manually Extracted Annotation is related to: LegumeIP is related to: Renal Disease Portal is related to: PhenoGO is related to: DOAF is related to: OBO is related to: biomaRt is related to: OncoboxPD is parent organization of: AmiGO is parent organization of: GOlr is parent organization of: RefGenome is parent organization of: OBO-Edit is parent organization of: OWLTools is parent organization of: Gene Ontology Tools is parent organization of: Gene Ontology Extension is parent organization of: SO is parent organization of: go-db-perl is parent organization of: go-perl works with: topGO works with: DIANA-mirPath works with: GOnet |
European Union QLRI-CT-2001-0098; European Union QLRI-CT-2001-00015; NHGRI P41 HG002273 |
PMID:23161678 PMID:10802651 |
Free, Freely available, Available for download | biotools:go, OMICS_02278, nif-0000-02915 | http://bioportal.bioontology.org/ontologies/GO https://bio.tools/go |
SCR_002811 | the Gene Ontology, GO, Gene Ontology Resource, Gene Ontology | 2026-02-14 02:00:32 | 10623 | ||||
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hot scan Resource Report Resource Website 1+ mentions |
hot scan (RRID:SCR_002840) | software resource | A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence. | software package, perl, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24860160 | Free, Freely available, Available for download | biotools:hot_scan, OMICS_05200 | https://bio.tools/hot_scan | SCR_002840 | hot_scan | 2026-02-14 02:00:33 | 6 | ||||||
|
GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr http://www.greenphyl.org/v3/ https://bio.tools/greenphyldb |
SCR_002834 | 2026-02-14 02:00:33 | 19 | ||||||
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FSL Resource Report Resource Website 1000+ mentions |
FSL (RRID:SCR_002823) | software resource, software library, software toolkit | Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. | dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation |
uses: Neuroimaging Data Model is used by: Spinal Cord Toolbox is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) is used by: XFSL: An FSL toolbox is used by: CMIND PY lists: SUSAN lists: FUGUE lists: Miscvis lists: BayCEST lists: ICA-PNM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Rodent Brain Extraction Tool is related to: Human Connectome Coordination Facility is related to: BASH4RfMRI is related to: DW-MRI registration in FSL is related to: FSL extensions is related to: Diffusion MRI of Traumatic Brain Injury is related to: Segmentation of Hippocampus Subfields is related to: masked ICA (mICA) Toolbox has parent organization: University of Oxford; Oxford; United Kingdom has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components has plug in: FMRI Expert Analysis Tool has plug in: FABBER has plug in: BASIL has plug in: VERBENA has plug in: Brain Extraction Tool has plug in: FMRIB's Automated Segmentation Tool has plug in: FMRIB’s Integrated Registration and Segmentation Tool has plug in: Harvard - Oxford Cortical Structural Atlas has plug in: FMRIB's Linear Image Registration Tool has plug in: FNIRT has plug in: FSLVBM has plug in: SIENA has plug in: SIENAX has plug in: Multimodal Image Segmentation Tool has plug in: Brain Intensity AbNormality Classification Algorithm has plug in: Multimodal Surface Matching has plug in: fsl_anat has plug in: FMRIB's Diffusion Toolbox has plug in: Tract Based Spatial Statistics has plug in: XTRACT has plug in: eddy has plug in: topup has plug in: eddyqc has plug in: randomise has plug in: PALM has plug in: fsl-cluster has plug in: FDR has plug in: DualRegression has plug in: FLOBS has plug in: FSLeyes has plug in: Fslutils has plug in: Atlasquery has plug in: MCFLIRT has plug in: POSSUM has plug in: FSL-MRS |
EPSRC ; MRC ; BBSRC ; GlaxoSmithKline ; Pfizer |
PMID:21979382 PMID:19059349 PMID:15501092 |
Free, Available for download, Freely available | nif-0000-00305, birnlex_2067, SCR_007368 | http://www.nitrc.org/projects/fsl http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ https://sources.debian.org/src/fsl/ |
SCR_002823 | , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library | 2026-02-14 02:00:32 | 4685 | |||||
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SMRT-Analysis Resource Report Resource Website 100+ mentions |
SMRT-Analysis (RRID:SCR_002942) | software resource | Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences. | software suite |
is listed by: OMICtools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05142 | http://www.pacb.com/devnet/ https://sources.debian.org/src/smrtanalysis/ |
SCR_002942 | SMRT Analysis | 2026-02-14 02:00:20 | 134 | |||||||
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Cancer Genome Anatomy Project Resource Report Resource Website 100+ mentions |
Cancer Genome Anatomy Project (RRID:SCR_003072) | CGAP | data or information resource, portal, topical portal | Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools | gene, gene expression, normal cell, precancer cell, cancer cell, cell, genome, anatomy, gene expression profile, tissue, pathway, rnai, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: National Cancer Institute is parent organization of: CGAP GO Browser |
Cancer, Normal, Precancer | NCI | Free, download Freely available | biotools:cgap, nif-0000-30468 | https://mitelmandatabase.isb-cgc.org/mb_search | SCR_003072 | Cancer Genome Anatomy Project (CGAP) | 2026-02-14 02:00:22 | 107 | ||||
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Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | data analysis service, analysis service resource, production service resource, source code, service resource, software resource | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-02-14 02:00:29 | 1673 | ||||
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tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-02-14 02:00:29 | 4 | ||||||
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BRAIN Resource Report Resource Website 10+ mentions |
BRAIN (RRID:SCR_003018) | software resource | Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23350948 | GNU General Public License, v2 | biotools:brain, OMICS_02410 | https://bio.tools/brain | SCR_003018 | Baffling Recursive Algorithm for Isotopic distributioN calculations, Baffling Recursive Algorithm for Isotope distributioN | 2026-02-14 02:00:21 | 44 | ||||||
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DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/ https://bio.tools/dialign-tx |
https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2026-02-14 02:00:21 | 43 | ||||
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SeWeR - SEquence analysis using WEb Resources Resource Report Resource Website |
SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) | portal, data or information resource, 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 | SEquence analysis using WEb Resources, SeWeR | 2026-02-14 02:00:56 | 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 | PERiodic seed Mapping, Periodic seed Mapping | 2026-02-14 02:00:38 | 60 | ||||||
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TAGS Resource Report Resource Website 100+ mentions |
TAGS (RRID:SCR_004294) | TAGS | data processing software, data analysis software, time-series analysis software, software application, software resource | 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 | 2026-02-14 02:00:57 | 139 | ||||||
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BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | data repository, storage service resource, data or information resource, service resource, database | 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 | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-02-14 02:00:42 | 29 | |||||
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SALT Resource Report Resource Website 1000+ mentions |
SALT (RRID:SCR_003187) | SALT | software resource | Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families. | next-generation sequencing, protein, protein domain, short read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23782615 | Free, Available for download, Freely available | OMICS_01565, biotools:salt | https://bio.tools/salt | SCR_003187 | SALT - Protein domain classifier | 2026-02-14 02:00:30 | 1294 | |||||
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PredictNLS Resource Report Resource Website 10+ mentions |
PredictNLS (RRID:SCR_003133) | PredictNLS | data analysis service, analysis service resource, production service resource, service resource, software resource | Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given. | bio.tools, nuclear localization signal, protein, protein sequence |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ROSTLAB has parent organization: Columbia University; New York; USA |
DOI:10.1093/embo-reports/kvd092 | Free, Available for download, Freely available | nif-0000-31416, OMICS_01633, SCR_008553, biotools:predictnls | https://www.rdocumentation.org/packages/propagate/versions/1.0-4/topics/predictNLS | SCR_003133 | Prediction and Analysis of Nuclear Localization Signals | 2026-02-14 02:00:22 | 30 | |||||
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LUMPY Resource Report Resource Website 100+ mentions |
LUMPY (RRID:SCR_003253) | data processing software, data analysis software, software application, software resource, simulation software, standalone software | Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed. | probabilistic, framework, structural, variant, discovery |
is listed by: OMICtools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
NHGRI R01 HG006693; NIH Office of the Director DP2 OD006493; Burroughs Wellcome Fund Career Award |
PMID:24970577 | Free, Available for download, Freely available | OMICS_04674 | https://sources.debian.org/src/lumpy-sv/ | SCR_003253 | lumpy-sv, LUMPY Express | 2026-02-14 02:00:24 | 447 | |||||
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NovelSeq Resource Report Resource Website |
NovelSeq (RRID:SCR_003136) | NovelSeq | software resource | Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. | sequence, insertion, genome sequencing, genome, next-generation sequencing, illumina, unix, linux, c, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:20385726 | Free, Available for download, Freely available | biotools:novelseq, nlx_156791, OMICS_02164 | https://mybiosoftware.com/novelseq-1-0-2-sequence-insertions-detection.html#google_vignette | SCR_003136 | NovelSeq: Novel Sequence Insertion Detection | 2026-02-14 02:00:30 | 0 | |||||
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mrCaNaVaR Resource Report Resource Website 10+ mentions |
mrCaNaVaR (RRID:SCR_003135) | mrCaNaVaR | software resource | Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals. | genome, next-generation sequence, duplication, deletion, copy number variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
Free, Freely available | OMICS_02138, nlx_156790, biotools:mrcanavar | https://bio.tools/mrcanavar | SCR_003135 | mrCaNaVaR - micro-read Copy Number Variant Regions, micro-read Copy Number Variant Regions | 2026-02-14 02:00:40 | 14 |
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