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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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cgpBattenberg Resource Report Resource Website 10+ mentions |
cgpBattenberg (RRID:SCR_017092) | data processing software, data analysis software, software application, software resource | Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data. | installation, helper, perl, wrapper, detect, subclonality, copy, number, NGS, next, generation, sequencing, data | is related to: battenberg | Free, Available for download, Freely available | SCR_017092 | 2026-08-01 12:06:02 | 11 | ||||||||||
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Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms. | assembler, single, molecule, sequencing, long, error, read, fast, accurate, genome, reconstruction, nucleotide, quality, data, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:27956617 | Free, Available for download, Freely available | biotools:Flye | https://bio.tools/Flye, https://sources.debian.org/src/flye/ | SCR_017016 | 2026-08-01 12:05:49 | 267 | |||||||
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Olympus: FluoView FV3000 Confocal Laser Scanning Microscope Resource Report Resource Website 50+ mentions |
Olympus: FluoView FV3000 Confocal Laser Scanning Microscope (RRID:SCR_017015) | instrument resource | FV3000 is a laser scanning confocal microscope system that captures high-resolution, high-contrast images by scanning samples point by point, enabling precise 3D fluorescence imaging. The system supports inverted and upright configurations and accommodates various objectives with magnifications ranging from 1.25× to 100×, including oil, silicone, and dry lenses, which allows imaging of both macro and micro-scale samples. It is equipped with multiple laser lines for excitation, including 405 nm, 488 nm, 561 nm, and 640 nm, as well as additional lines in some configurations (445 nm, 514 nm, 594 nm, 630 nm), enabling the use of several fluorophores simultaneously. On the detection side, the microscope uses high-sensitivity photomultiplier tube detectors, including GaAsP PMTs and multi-alkali PMTs. | instrument, Olympus, confocal, laser, scanning, microscope, Fluoview, FV3000 |
is used by: Texas State University Nanofabrication Research Service Center Core Facility is provided by: Olympus |
Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_017015.pdf | https://www.olympus-global.com/technology/design/product/fv3000_series.html | https://www.olympus-lifescience.com/en/laser-scanning/fv3000 | SCR_017015 | , Olympus FV3000 Confocal, Olympus FV3000 microscope, FLUOVIEW FV3000 | 2026-08-01 12:05:59 | 51 | ||||||
|
BBmap Resource Report Resource Website 500+ mentions |
BBmap (RRID:SCR_016965) | image analysis software, software toolkit, alignment software, software application, data processing software, software resource | Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform. | Joint Genome Institute, short, read, aligner, DNA, RNA, sequencing, data, large, genome, scaffold, mutated, long, indel |
is listed by: Bestus Bioinformaticus Tools is listed by: Debian is related to: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/, https://sources.debian.org/src/bbmap/ | SCR_016965 | 2026-08-01 12:05:47 | 797 | |||||||||
|
TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | software toolkit, data analysis software, software application, software resource, data processing software | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-08-01 12:05:44 | 10 | ||||||
|
Experimental Design Assistant Resource Report Resource Website 100+ mentions |
Experimental Design Assistant (RRID:SCR_017019) | EDA | software resource, web application, service resource | Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility. | in vivo, design, conduct, analysis, reporting, animal, experiment, irreproducibility, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NC3Rs |
PMID:28957312 | Free, Freely available | biotools:eda | https://bio.tools/eda | SCR_017019 | EDA, Experimental Design Assistant (EDA), Experimental Design Assistant | 2026-08-01 12:05:49 | 187 | |||||
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CCTOP Resource Report Resource Website 10+ mentions |
CCTOP (RRID:SCR_016963) | CCTOP | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them. | transmembrane, topology, prediction, signal, peptide, globular, protein, discrimination, amino, acid, sequence, region, orientation, segment, bio.tools |
is listed by: Debian is listed by: bio.tools works with: PDBTM works with: Topology Data Bank of Transmembrane Proteins works with: TopDom |
Hungarian Scientific Research Fund | PMID:25943549 | Free, Freely available | biotools:cctop | https://bio.tools/cctop | SCR_016963 | CCTOP, Consensus Constrained TOPology | 2026-08-01 12:05:57 | 29 | ||||
|
LION/web Resource Report Resource Website 10+ mentions |
LION/web (RRID:SCR_017018) | Lipid Ontology (LION) | data analysis service, web application, service resource, production service resource, software resource, analysis service resource | Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way. | lipid, ontology, enrichment, lipidomic, data, analysis, biophysical | is related to: Utrecht University; Utrecht; Netherlands | DOI:10.1101/398040 | Free, Freely available | SCR_017018 | The Lipid Ontology (LION), Lipid Ontology, LIpid ONtology (LION), LIpid ONtology, LION | 2026-08-01 12:05:59 | 21 | |||||||
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Anima Resource Report Resource Website 10+ mentions |
Anima (RRID:SCR_017017) | image analysis software, data or information resource, software toolkit, mri 3d image, portal, data analysis software, diffusion-weighted mri 3d image, image, software application, software resource, registration software, data processing software, image processing software, 3d spatial image | Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows. | medical, image, processing, analysis, registration, statistical, quantitative, MRI, data, VISAGES |
is related to: Anima scripts is related to: Empenn has parent organization: VISAGES Research |
Free, Freely available, Available for download | http://olivier.commowick.org/software_anima.php | SCR_017017 | 2026-08-01 12:05:45 | 15 | |||||||||
|
dndSCV Resource Report Resource Website 10+ mentions |
dndSCV (RRID:SCR_017093) | data processing software, data analysis software, software application, software resource | Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets. | dN/dS, method, quantify, selection, cancer, somatic, evolution, missense, nonsense, essential, splice, mutation, gene, genome, dataset |
uses: devtools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017093 | 2026-08-01 12:05:52 | 35 | ||||||||||
|
GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | data processing software, data analysis software, software application, software resource | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-08-01 12:05:45 | 50 | |||||||||
|
Comparative Metatranscriptomics Workflow Resource Report Resource Website 1+ mentions |
Comparative Metatranscriptomics Workflow (RRID:SCR_017109) | CoMW | data or information resource, data analysis software, workflow, narrative resource, software application, software resource, sequence analysis software, data processing software, training material | Software tool for standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. Used for classification of these reads using assembled contigs to reference databases. | workflow, functionally, classify, mRNA, metatranscriptomic, RNA, next, generation, sequencing, NGS, short, read, assembly, contig, reference, database, bio.tools |
is listed by: bio.tools is listed by: Debian |
h2020 EU MicroArctic ITN | Free, Available for download, Freely available | biotools:comw | https://bio.tools/CoMW | SCR_017109 | 2026-08-01 12:06:02 | 3 | ||||||
|
Empenn Resource Report Resource Website |
Empenn (RRID:SCR_017074) | project portal, data or information resource, portal, community building portal, topical portal, disease-related portal | Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts. | biomedical, image, analysis, disease, medical, imaging, neuroinformatics, population, cohort, brain, neurological, disorder |
is related to: Anima scripts is related to: VISAGES Research is related to: University of Rennes 1; Rennes; France is related to: Anima |
SCR_017074 | Brain | 2026-08-01 12:05:51 | 0 | ||||||||||
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Source code for analysis of GC-MS data - Rice HxD Project Resource Report Resource Website 1+ mentions |
Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) | data visualization software, data analysis software, source code, software application, software resource, data processing software | Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress. | analysis, GC-MS, data, rice, sample, statistics, workflow | Free, Available for download, Freely available | SCR_017073 | 2026-08-01 12:06:01 | 1 | |||||||||||
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Anima scripts Resource Report Resource Website 10+ mentions |
Anima scripts (RRID:SCR_017072) | software resource, software application, image processing software, data processing software | Open source scripts for medical image processing. Provides set of scripts in Python shell. These scripts use essentially tools from Anima to perform more complex series like image preprocessing, model estimation, atlas creation. | medical, image, processing, analysis, registration, atlas, diffusion, MRI |
is related to: Anima is related to: Empenn is related to: Python Programming Language has parent organization: VISAGES Research |
Free, Available for download, Freely available | https://anima.irisa.fr | SCR_017072 | 2026-08-01 12:05:51 | 12 | |||||||||
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RNAmmer Resource Report Resource Website 100+ mentions |
RNAmmer (RRID:SCR_017075) | data analysis service, data analysis software, data access protocol, service resource, software application, data processing software, production service resource, software resource, analysis service resource, standalone software, web service | Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. | predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA | has parent organization: Technical University of Denmark; Lyngby; Denmark | EMBIO at the University of Oslo ; Research Council of Norway ; Danish Center for Scientific Computing ; European Union |
PMID:17452365 | Restricted | SCR_017075 | 2026-08-01 12:05:45 | 103 | ||||||||
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VORTEX Resource Report Resource Website 10+ mentions |
VORTEX (RRID:SCR_017047) | data processing software, data analysis software, software application, software resource | Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids. | single, cell, analysis, clustering, visualization, nonparametric, density, based, X shift | has parent organization: Stanford University; Stanford; California | PMID:27183440 | Free, Available for download, Freely available | http://web.stanford.edu/~samusik/vortex/ | SCR_017047 | VorteX Clustering Environment | 2026-08-01 12:05:50 | 19 | |||||||
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HaTSPiL Resource Report Resource Website 1+ mentions |
HaTSPiL (RRID:SCR_017059) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability. | next, generation, sequencing, pipeline, metadata, analysis, mutation, barcoding, customisability, modularity, bio.tools |
uses: Python Programming Language is listed by: Debian is listed by: bio.tools has parent organization: Italian Institute for Genomic Medicine; Turin; Italy |
Free, Available for download, Freely available | biotools:HatSPiL | https://bio.tools/HaTSPiL | SCR_017059 | 2026-08-01 12:05:45 | 1 | ||||||||
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BioPortainer Resource Report Resource Website 1+ mentions |
BioPortainer (RRID:SCR_017058) | data processing software, data analysis software, software application, software resource | Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application. | docker, bioportainer, user, interaction, docker, environment, infrastructure, platform, application | Free, Available for download, Freely available | https://github.com/BioPortainer/BioPortainer | SCR_017058 | BioPortainer Workbench | 2026-08-01 12:06:01 | 1 | |||||||||
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PRSice Resource Report Resource Website 50+ mentions |
PRSice (RRID:SCR_017057) | data processing software, data analysis software, software application, software resource | Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux. | polygenic, risk, score, calculating, applying, plotting, result, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
EU ; NIHR Biomedical Research Centre |
PMID:25550326 | Free, Available for download, Freely available | OMICS_23656, biotools:prsice | https://choishingwan.github.io/PRSice/, https://bio.tools/prsice | SCR_017057 | prsice, PRSice-2, Polygenic Risk Score software, PRSice1, PRSice2 | 2026-08-01 12:05:50 | 97 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
