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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Science Dynamics Resource Report Resource Website 1+ mentions |
Science Dynamics (RRID:SCR_016958) | project portal, numeric dataset, portal, data or information resource, data set | Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks. | Science, Dynamics, project, dataset, code, framework, optimization, academic, publishing, metric, observing, Goodhart, Law, action, journal, network | has parent organization: University of Washington; Seattle; USA | e Washington Re-search Foundation Fund for Innovation in Data-Intensive Discovery ; Moore/Sloan Data Science Environments Project at the University of Washington ; Microsoft Azure Research Award |
Free, Freely available | https://www.ise.bgu.ac.il/labs/fire/sciencedynamics/index.html | SCR_016958 | 2026-08-14 09:27:54 | 1 | ||||||||
|
Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | software toolkit, data processing software, software application, data analysis software, software resource, sequence analysis 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 | 2026-08-14 09:27:31 | 324 | |||||||
|
BBmap Resource Report Resource Website 500+ mentions |
BBmap (RRID:SCR_016965) | software toolkit, image analysis software, data processing software, software application, software resource, alignment software | 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 | 2026-08-14 09:27:54 | 915 | |||||||||
|
TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | software toolkit, data processing software, software application, data analysis software, software resource | 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 | 2026-08-14 09:27:30 | 11 | ||||||
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CCTOP Resource Report Resource Website 10+ mentions |
CCTOP (RRID:SCR_016963) | CCTOP | production service resource, web service, data access protocol, software resource, service resource, 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 | 2026-08-14 09:27:40 | 31 | ||||
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LION/web Resource Report Resource Website 10+ mentions |
LION/web (RRID:SCR_017018) | Lipid Ontology (LION) | production service resource, data analysis service, web application, software resource, service 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 | 2026-08-14 09:27:40 | 33 | |||||||
|
Anima Resource Report Resource Website 10+ mentions |
Anima (RRID:SCR_017017) | software toolkit, diffusion-weighted mri 3d image, image processing software, data processing software, image analysis software, portal, image, data or information resource, data analysis software, software application, mri 3d image, 3d spatial image, software resource, registration software | 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 | 2026-08-14 09:27:55 | 20 | |||||||||
|
Illuminating the Druggable Genome Resource Report Resource Website 50+ mentions |
Illuminating the Druggable Genome (RRID:SCR_016924) | IDG | data repository, storage service resource, portal, data or information resource, consortium, service resource, organization portal | Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC). | understudied, target, protein, G protein, coupled, receptor, ion, channel, kinase, bio.tools |
is recommended by: National Library of Medicine is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian |
NIH Common Fund | biotools:pharos | https://pharos.nih.gov/, https://bio.tools/pharos, https://darkmatter.ucsf.edu/about | https://druggablegenome.net | SCR_016924 | Pharos, Illuminating the Druggable Genome, IDG, Illuminating Druggable Genome | 2026-08-14 09:27:30 | 64 | |||||
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The Human BioMolecular Atlas Program Resource Report Resource Website 10+ mentions |
The Human BioMolecular Atlas Program (RRID:SCR_016922) | HuBMAP | funding resource, data or information resource, portal, project portal | Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows. | organism, cell, tissue, data, generation, technology, organization, functional, mapping, human, body |
uses: Azimuth is listed by: NIDDK Information Network (dkNET) is related to: HuBMAP Data Portal |
NIH | https://humanatlas.io/omap, https://avr.hubmapconsortium.org/, https://commonfund.nih.gov/HuBMAP, https://zenodo.org/records/5244551 | SCR_016922 | Human BioMolecular Atlas Program, HuBMAP, The Human BioMolecular Atlas Program, NIH HuBMAP | 2026-08-14 09:27:39 | 26 | |||||||
|
Digital Expression Explorer 2 Project Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Project (RRID:SCR_016929) | DEE2 | database, data repository, project portal, storage service resource, portal, data or information resource, service resource | Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes. | transcriptome, database, RNA-seq, sequencing, processed, data |
is related to: Digital Expression Explorer 2 Source Code is related to: Digital Expression Explorer 2 Docker Image |
DOI:10.5281/zenodo.1561840 | Free, Freely available | SCR_016929 | DEE2 Project | 2026-08-14 09:27:39 | 4 | |||||||
|
ALGGEN-PROMO Resource Report Resource Website 100+ mentions |
ALGGEN-PROMO (RRID:SCR_016926) | laboratory portal, data processing software, portal, data or information resource, data analysis software, software application, software resource, sequence analysis software, service resource, organization portal | Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches. | identify, transcription, factor, binding, site, DNA, sequence, species, regulatory, element, search | PMID:11847087 PMID:12824386 |
Free, Available for download, Freely available | SCR_016926 | PROMO, ALGorithmics and GENetics PROMO, ALGGEN, ALGGEN-PROMO | 2026-08-14 09:27:53 | 434 | |||||||||
|
FibrilTool Resource Report Resource Website 1+ mentions |
FibrilTool (RRID:SCR_016773) | image analysis software, data processing software, software application, data analysis software, data analytics software, software resource | ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Used to evaluate the orientation of fiber orientation pattern and plots the results in the image. | quantify, fibrillar, structure, raw, image, microscopy | is listed by: BISE | Institut National de la Recherche Agronomique (INRA) ; France ; Ministry of Science and Higher Education ; Poland ; National Science Centre ; Poland ; Agence Nationale de la Recherche |
PMID:24481272 | Free, Available for download, Freely available to the scientific community | SCR_016773 | 2026-08-14 09:27:29 | 5 | ||||||||
|
smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | data processing software, software application, data analysis software, software resource | Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required. | nucleotide, DNA, read, unique, molecular, identifier, single, inversion, probe, data, analysis, mutation, sequence | requires: SAMTOOLS | Free, Available for download, Freely available | SCR_016892 | single molecule Molecular Inversion Probesfil, smMIPfil | 2026-08-14 09:27:52 | 2 | |||||||||
|
Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | software toolkit, data processing software, software application, data analysis software, software resource | Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging. | automated, processing, analysis, visualization, data, acquired, single, molecule, localization, microscopy, SMLM, imaging, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: ImageJ |
Czech Science Foundation ; Charles University ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | 2026-08-14 09:27:39 | 48 | |||||
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CCTop Resource Report Resource Website 100+ mentions |
CCTop (RRID:SCR_016890) | data processing software, web application, software application, data analysis software, software resource, service resource | Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. | CRISPR, Cas9, target, prediction, sgRNA, site, data | is related to: Python Programming Language | European Research Council ; German Research Foundation |
PMID:25909470 | SCR_016890 | 2026-08-14 09:27:39 | 130 | |||||||||
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Culture Collection of Algae at the University of Texas Resource Report Resource Website 10+ mentions |
Culture Collection of Algae at the University of Texas (RRID:SCR_016782) | UTEX | database, storage service resource, portal, biospecimen repository, data or information resource, service resource, organization portal, material storage repository | The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world. | culture, collection, algae | has parent organization: University of Texas at Austin; Texas; USA | U.S. National Science Foundation ; College of Natural Sciences of The University of Texas at Austin |
Commercially available | SCR_016782 | The UTEX Culture Collection of Algae, Culture Collection of Algae at the University of Texas, UTEX | 2026-08-14 09:27:29 | 33 | |||||||
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CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Basic Research Program of China ; Program for New Century Excellent Talents in University ; Fundamental Research Funds for the Central Universities |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2026-08-14 09:27:53 | 42 | |||||
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ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data processing software, software application, data analysis software, software resource | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-08-14 09:27:39 | 42 | |||||
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EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, software application, image processing software, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-08-14 09:27:52 | 107 | |||
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Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data processing software, software application, data analysis software, software resource | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | PyClone | 2026-08-14 09:27:39 | 46 |
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