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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Graph2GO Resource Report Resource Website 1+ mentions |
Graph2GO (RRID:SCR_018726) | data analysis software, data processing software, software resource, software application | Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology. | Protein function prediction, graph neural network, attributed network embedding, representation learning, multi-modal model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ohio State University College of Medicine; Ohio; USA |
Free, Available for download, Freely available | SCR_018727, biotools:graph2go | https://integrativeomics.shinyapps.io/graph2go/, https://bio.tools/graph2go | SCR_018726 | 2026-08-13 09:30:07 | 2 | ||||||||
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iMol Resource Report Resource Website 1+ mentions |
iMol (RRID:SCR_018735) | data processing software, software resource, data visualization software, software application | Software molecular visualization application for Mac OS X operating system. Tool for chemists and molecular biologists used for handling small and large molecules, loading multiple molecules, moving and rotating them independently, or displaying molecular dynamics trajectory. Allows loading molecules using file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO. | Molecular visualization, Mac OS X operating system, molecule, loading molecule, moving molecule, rotating molecule, displaying dynamics trajectory | Free, Available for download, Freely available | SCR_018735 | 2026-08-13 09:30:15 | 1 | |||||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-08-13 09:30:15 | 4 | ||||||||
|
TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features. | Tumor, tumor infiltrating immune cell, immune cell, cell, analysis, cancer cell, cancer type, tumor immunological feature, tumor genomic feature, display | National Natural Science Foundation of China ; NCI CA180980; Dana-Farber Cancer Institute |
PMID:29092952 | Free, Freely available | SCR_018737 | Tumor IMmune Estimation Resource | 2026-08-13 09:30:28 | 3010 | |||||||
|
Imspector Resource Report Resource Website 50+ mentions |
Imspector (RRID:SCR_018863) | data analysis software, data processing software, software resource, software application | Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results. | Data analysis, real time data, visualization, quantitative analysis, microscopy, spectroscopy | Free, Freely available | https://github.com/AbberiorInstruments/ImspectorDocs/blob/master/docs/intro.rst, https://imspector.abberior-instruments.com/ | SCR_018863 | 2026-08-13 09:30:17 | 85 | ||||||||||
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Repetier Host Resource Report Resource Website 10+ mentions |
Repetier Host (RRID:SCR_018901) | data processing software, software application, 3d visualization software, data visualization software, software resource | Open source 3D printing software which supports multi part printing and has slicers. | 3D printing, multi part printing support, slicer, data visualization, 3D visualization | Free, Available for download, Freely available | SCR_018901 | Repetier-Host | 2026-08-13 09:30:31 | 41 | ||||||||||
|
rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | rVista 2.0 | 2026-08-13 09:30:07 | 34 | ||||||
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TRACESPipe Resource Report Resource Website 1+ mentions |
TRACESPipe (RRID:SCR_018831) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data. | Hybrid pipeline, genome reconstruction, genome analysis, viral genome, host genome, multi organ sequencing, multi organ level, DNA sequence data, multiple organ data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.5524/100771 | Free, Freely available | biotools:tracespipe | http://dx.doi.org/10.5524/100771, https://bio.tools/tracespipe | SCR_018831 | 2026-08-13 09:30:30 | 2 | |||||||
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Simple Assignment of Spots to Surfaces Resource Report Resource Website 1+ mentions |
Simple Assignment of Spots to Surfaces (RRID:SCR_018797) | SASS | data analysis software, data processing software, software resource, software application | Software tool as custom analysis code combining single-cell traces and spot detection from live imaging movies and using Imaris output. | Custom analysis, single cell trace, spot detection, live imaging movie, assign spots, Imaris detection, expression domain, cell distance |
uses: Imaris has parent organization: University of Manchester; Manchester; United Kingdom |
DOI:10.1101/837179 | Free, Available for download, Freely available | SCR_018797 | 2026-08-13 09:30:16 | 7 | ||||||||
|
FunCoup Resource Report Resource Website 1+ mentions |
FunCoup (RRID:SCR_018711) | data or information resource, data access protocol, database, service resource, web service, software resource | Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search. | Genome, genome functional coupling network, coupling network, functional coupling, functional couplings search, gene identifier, genome data | has parent organization: Karolinska Institute; Stockholm; Sweden | Swedish Research Council ; Stockholm University |
PMID:24185702 | Free, Freely available | SCR_018711 | 2026-08-13 09:30:27 | 3 | ||||||||
|
NGScloud2 Resource Report Resource Website 1+ mentions |
NGScloud2 (RRID:SCR_018716) | data analysis software, data processing software, software resource, software application | Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species. | RNAseq analysis, non model species, cloud computing, AWS, spot instances, RNAseq, RADseq, functional annotation, plant | Spanish National Parks Agency Ministry of Agriculture ; Spanish Ministry of Economy and Competitiveness ; Amazon Research Grant |
PMID:29726914 | Free, Available for download, Freely available | https://github.com/GGFHF/NGScloud/ | SCR_018716 | NGScloud | 2026-08-13 09:30:15 | 1 | |||||||
|
CONSORT Resource Report Resource Website 100+ mentions |
CONSORT (RRID:SCR_018720) | CONSORT | data or information resource, organization portal, narrative resource, standard specification, portal | Standards for transparent trials reporting. Encompasses various initiatives developed by CONSORT Group to alleviate problems arising from inadequate reporting of randomized controlled trials. Main product of CONSORT is CONSORT Statement, which is evidence based, minimum set of recommendations for reporting randomized trials. CONSORT Statement is endorsed by medical journals and leading editorial organizations. | MDAR, standard, transparent trial, trial reporting, CONSORT group, controlled trial, CONSORT Statement, randomized trials reporting, medical journal, editorial organization, reporting | is related to: CONSORT TM | Medical Research Council ; Family Health International ; University of Oxford ; Ottawa Hospital Research Institute |
Free, Freely available | SCR_018720 | Consolidated Standards of Reporting Trials | 2026-08-13 09:30:28 | 389 | |||||||
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Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | data analysis software, data processing software, software application, software toolkit, software resource | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NIH Office of the Director DP2 OD00667; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NHGRI P50 HG006193; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2026-08-13 09:30:07 | 342 | ||||||
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D-GENIES Resource Report Resource Website 50+ mentions |
D-GENIES (RRID:SCR_018967) | web application, data processing software, software application, image analysis software, alignment software, standalone software, software resource | Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. | bio.tools |
uses: Minimap2 is listed by: Debian is listed by: bio.tools |
PMID:29888139 | Free, Available for download, Freely available | biotools:d-genies | https://github.com/genotoul-bioinfo/dgenies, https://bio.tools/d-genies | SCR_018967 | Dot plot large GENomes in an Interactive, Efficient and Simple way | 2026-08-13 09:30:32 | 56 | ||||||
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MicroFilePlus Resource Report Resource Website 1+ mentions |
MicroFilePlus (RRID:SCR_018724) | image processing software, data processing software, software resource, software application | Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources. | Image file format, image converter, converter, OME-TIFF Format, jpeg2000, jpx, JP2, MBF Bioscience | Restricted | SCR_018724 | MicroFilePlus, MicroFile+, microfileplus | 2026-08-13 09:30:28 | 2 | ||||||||||
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Robetta Resource Report Resource Website 100+ mentions |
Robetta (RRID:SCR_018805) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure. | Protein structure prediction, protein, structure prediction, prediction service, automated prediction, analysis tools, genomic data, protein sequence, protein model, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:15215442 | Restricted | biotools:robetta | https://bio.tools/robetta | SCR_018805 | 2026-08-13 09:30:29 | 487 | |||||||
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FALCON Resource Report Resource Website 100+ mentions |
FALCON (RRID:SCR_018804) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web tool as high throughput protein structure prediction service. High throughput server for protein structure prediction. | Protein structure, protein structure prediction, simulation, 3D structure, protein, high throughput protein, structure prediction | Restricted | SCR_018804 | FALCON@home | 2026-08-13 09:30:09 | 432 | ||||||||||
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Long Ranger Resource Report Resource Website 10+ mentions |
Long Ranger (RRID:SCR_018925) | data analysis software, data processing software, software application, software toolkit, software resource | Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics. | Analysis pipelines, process chromium sequencing output, align reads, call SNPs, phase SNPs, indel, structural variant, 10x Genomics | Restricted | SCR_018925 | 2026-08-13 09:30:32 | 14 | |||||||||||
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WEBMAXC EXTENDED Resource Report Resource Website 10+ mentions |
WEBMAXC EXTENDED (RRID:SCR_018807) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web tool for computing metal ion concentrations in physiological solutions. Used for determining free metal concentration in presence of chelators or total metal given desired free concentration. | Metal ion concentration, physiological solution, free metal concentration, chelator, free concentration, free metal concentration calculation |
is related to: MAXCHELATOR has parent organization: Stanford University; Stanford; California |
Free, Freely available | SCR_018807 | WEBMAXC Extended | 2026-08-13 09:30:16 | 24 | |||||||||
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C-IMMSIM Resource Report Resource Website 1+ mentions |
C-IMMSIM (RRID:SCR_018775) | data access protocol, software resource, service resource, web service | Web prediction tool for molecular binding in simulation of immune system. Agent based simulator of immune response that represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction.Calculates immune response to generic pathogenic secondary structure. Allows users to submit antigen protein sequence and specify schedule of its injection as well as host haplotype. | Molecular binding prediction, molecular binding simulation, immune system, pathogen, lymphocyte receptor, amino acid sequence, T cell epitope prediction, B cell epitope prediction, calculate immune response, generic pathogenic secondary structure, antigen protein sequence, host haplotype, immunogenic part, invading pathogen | European Community | PMID:20419125 | Restricted | SCR_018775 | 2026-08-13 09:30:08 | 5 |
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