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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Gsnap2Augustus Resource Report Resource Website 1+ mentions |
Gsnap2Augustus (RRID:SCR_017555) | software application, simulation software, software resource | Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap. | Generate, hint, Augustus, gene, prediction, mapping, Gsnap |
uses: GSNAP works with: Augustus |
Free, Available for download, Freely available | SCR_017555 | 2026-08-14 09:28:08 | 1 | ||||||||||
|
Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | data processing software, software application, data analysis software, software resource | Software tool for de novo transcriptome assembly from RNA-Seq data. | de novo, transcriptome, assembly, RNAseq, data |
has parent organization: University of Washington; Seattle; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Stanford University; Stanford; California |
NSF Center for Science of Information ; NHGRI ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | 2026-08-14 09:27:31 | 2 | ||||||||
|
NiMARE Resource Report Resource Website 10+ mentions |
NiMARE (RRID:SCR_017398) | NiMARE | data processing software, software application, data analysis software, software resource | Software Python package for coordinate and image based meta analysis of neuroimaging data. | Coordinate, image, based, meta, analysis, neuroimaging, data |
uses: PyMARE is used by: Neurosynth Compose |
Free, Available for download, Freely available | https://nimare.readthedocs.io/en/latest/ | SCR_017398 | Neuroimaging Meta Analysis Research Environment, Neuroimaging Meta-Analysis Research Environment | 2026-08-14 09:28:05 | 17 | |||||||
|
NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | simulation software, data processing software, software application, data analysis software, software resource | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-08-14 09:27:40 | 45 | ||||||||
|
ngsRelate Resource Report Resource Website 1+ mentions |
ngsRelate (RRID:SCR_016588) | data processing software, software application, data analysis software, software resource | Software tool for estimating pairwise relatedness from next-generation sequencing data. | estimating, pairwise, relatedness, next, generation, sequencing, data, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
Danish National Research Foundation ; Danish Council for Independent Research |
PMID:26323718 | Free, Available for download, Freely available | biotools:ngsRelateV2, biotools:ngsrelate | https://bio.tools/ngsRelateV2, https://bio.tools/ngsrelate | http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694 | SCR_016588 | ngsRelateV2 | 2026-08-14 09:27:46 | 6 | ||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data processing software, software application, data analysis software, software resource, data visualization software | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Cancer Research Center-Heidelberg Center for Personalized Oncology ; BMBF |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | 2026-08-14 09:27:35 | 3949 | ||||||
|
Seurat Resource Report Resource Website 10000+ mentions |
Seurat (RRID:SCR_016341) | software toolkit, data processing software, software application, data analysis software, software resource | Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is used by: scSidekick is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | 2026-08-14 09:27:41 | 11480 | |||||||
|
LTRpred Resource Report Resource Website 1+ mentions |
LTRpred (RRID:SCR_017031) | data processing software, software application, data analysis software, data analytics software, software resource | Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format. | LTR, retrotransposon, prediction, genome, assembly, functional, annotation | is related to: R Project for Statistical Computing | Free, Available to download, Freely available | https://hajkd.github.io/LTRpred/ | SCR_017031 | LTRpred(ict) | 2026-08-14 09:27:31 | 6 | ||||||||
|
Conserved Domains Search Resource Report Resource Website 1000+ mentions |
Conserved Domains Search (RRID:SCR_018729) | web service, data or information resource, data access protocol, software resource, service resource | Web tool for conserved domains searching within protein or coding nucleotide sequence. | Conserved domain, protein, coding nucleotide sequence, domain search, domain, nucleotide sequence | works with: Conserved Domain Database | Free, Freely available | SCR_018729 | CD-search | 2026-08-14 09:27:57 | 2002 | |||||||||
|
Graph2GO Resource Report Resource Website 1+ mentions |
Graph2GO (RRID:SCR_018726) | data processing software, software application, data analysis software, software resource | 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 | 2026-08-14 09:28:23 | 2 | ||||||||
|
iMol Resource Report Resource Website 1+ mentions |
iMol (RRID:SCR_018735) | data processing software, data visualization software, software application, software resource | 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 | 2026-08-14 09:28:06 | 1 | |||||||||||
|
LUNGevity Resource Report Resource Website 1+ mentions |
LUNGevity (RRID:SCR_018570) | organization portal, data or information resource, funding resource, portal | Portal dedicated to funding lung cancer research by LUNGevity Foundation. Supports patient focused research and convene multi stakeholder meetings to streamline research process and accelerate progress to patients. Seeks to empower patients to be active decision makers in their treatment process through educational resources, online peer-to-peer support, and in-person survivorship programs. | Funding lung cancer, funding, lung cancer, LUNGevity Foundation, patient focused research support | lung cancer | Restricted | SCR_018570 | 2026-08-14 09:27:56 | 3 | ||||||||||
|
Intensity Ratio Nuclei Cytoplasm Tool Resource Report Resource Website 10+ mentions |
Intensity Ratio Nuclei Cytoplasm Tool (RRID:SCR_018573) | image processing software, image analysis software, data processing software, software application, software resource | Software tool to calculate ratio of intensity in nuclei and cytoplasm. It needs two images as input cytoplasm channel and nuclei channel. | Intensity ratio, nuclei, cytoplasm, image, cytoplasm channel, nuclei channel, calculate ration, ImageJ | works with: ImageJ | Free, Freely available | SCR_018573 | 2026-08-14 09:28:04 | 37 | ||||||||||
|
piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | production service resource, web service, data access protocol, software resource, service resource, analysis service 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 | 2026-08-14 09:27:57 | 4 | ||||||||
|
TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | production service resource, web service, data access protocol, software resource, service resource, analysis service 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 | 2026-08-14 09:28:23 | 3010 | |||||||
|
Imspector Resource Report Resource Website 50+ mentions |
Imspector (RRID:SCR_018863) | data processing software, software application, data analysis software, software resource | 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 | 2026-08-14 09:28:24 | 85 | ||||||||||
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Repetier Host Resource Report Resource Website 10+ mentions |
Repetier Host (RRID:SCR_018901) | data processing software, software application, software resource, data visualization software, 3d visualization software | 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 | 2026-08-14 09:27:59 | 41 | ||||||||||
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rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | production service resource, web service, data access protocol, software resource, service resource, analysis service 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 | 2026-08-14 09:28:23 | 34 | ||||||
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TRACESPipe Resource Report Resource Website 1+ mentions |
TRACESPipe (RRID:SCR_018831) | data processing software, software application, data analysis software, 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 | 2026-08-14 09:27:59 | 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 processing software, software application, data analysis software, software resource | 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 | 2026-08-14 09:28:23 | 7 |
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