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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Galaxy scater Resource Report Resource Website 1+ mentions |
Galaxy scater (RRID:SCR_017394) | data analysis software, data processing software, software application, software toolkit, service resource, source code, training service resource, software resource, sequence analysis software | Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses. | scRNA-seq, single, cell, scater, Galaxy, training, quality, control, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC BBS/E/T/000PR9817; BBSRC BBS/E/T/000PR9818; BBSRC BBS/E/T/000PR9819; BBSRC CCG:BBS/E/T/000PR9816 |
DOI:10.1101/724047 | Free, Available for download, Freely available | biotools:Galaxy_scater | https://bio.tools/Galaxy_scater | SCR_017394 | 2026-08-13 09:30:00 | 1 | ||||||
|
Webcutter Resource Report Resource Website 10+ mentions |
Webcutter (RRID:SCR_017638) | data analysis software, data processing software, data access protocol, software application, analysis service resource, production service resource, service resource, web service, data analysis service, software resource, sequence analysis software | Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences. Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis. | Find, restriction, site, endonuclease, map, nucleotide, DNA, sequence, degenarte, digest, silent, mutagenesis |
has parent organization: Yale University; Connecticut; USA works with: GenBank works with: REBASE |
Free, Freely available | SCR_017638 | Webcutter 2.0, Webcutter 2 | 2026-08-13 09:30:04 | 15 | |||||||||
|
Multiple Myeloma survival predictor Resource Report Resource Website 1+ mentions |
Multiple Myeloma survival predictor (RRID:SCR_017651) | data access protocol, software resource, service resource, web service | Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3. | Multiple Myeloma, prognostic model, survival analysis, GuanRank, bio.tools |
is listed by: bio.tools is listed by: Debian |
Multiple Myeloma | Restricted | biotools:Multiple_Myeloma_survival_prediction | https://bio.tools/Multiple_Myeloma_survival_prediction | SCR_017651 | 2026-08-13 09:30:04 | 2 | |||||||
|
GeneLab Resource Report Resource Website 10+ mentions |
GeneLab (RRID:SCR_017658) | GLDS | data or information resource, database, service resource, data repository, storage service resource | Omics database for spaceflight experiments. Interactive, open access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Enables exploration of molecular network responses of terrestrial biology to space environment. Contains curated omics data, metadata and radiation dosimetry for model organisms. Supports standard guidelines for submission of datasets, MIAME for microarray, ENCODE Consortium Guidelines for RNA-seq and MIAPE Guidelines for proteomics. | Omics, spaceflight, experiment, data, system, bioinformatic, repository, terrestrial, biology, space, radiation, dosimetry, model, organism, standard, guideline, submission, dataset |
uses: MIAME is related to: NASA Science |
Space Life and Physical Sciences Division at NASA Headquarters | PMID:30329036 | r3d100013680 | https://www.nasa.gov/centers-and-facilities/ames/what-is-nasas-genelab/, https://doi.org/10.17616/R31NJN1S | SCR_017658 | GeneLab Data System | 2026-08-13 09:29:46 | 35 | |||||
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MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | data analysis software, data processing software, software application, software toolkit, software resource, sequence analysis software | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/, https://bio.tools/MCScan | SCR_017650 | Multiple Collinearity Scan | 2026-08-13 09:30:05 | 42 | |||||||
|
Blackfynn Discover Resource Report Resource Website 1+ mentions |
Blackfynn Discover (RRID:SCR_018068) | data or information resource, database, service resource, data repository, storage service resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. Data repository for scientific data. Open data library to explore neuroscience data for neurodegenerative diseases for which there are no disease modifying treatments. | Neuroscience data, data repository, neurogenerative disease |
is used by: SPARC Portal is related to: Pennsieve Data Management Platform is organization facet of: SPARC Portal |
epilepsy, Parkinson, Alzheimer, neurodegenerative disease | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_018068 | 2026-08-13 09:29:57 | 1 | |||||||||
|
Blobtools Resource Report Resource Website 100+ mentions |
Blobtools (RRID:SCR_017618) | data processing software, software application, data visualization software, data analytics software, software resource | Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants. | Modular, command, line, solution, visualisation, quality, control, taxonomic, partitioning, genome, dataset, genome assembly, screening, contaminant, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BlobTools2 |
James Hutton Institute/Edinburgh University School of Biological Sciences fellowship ; BBSRC |
DOI:10.12688/f1000research.12232.1 | Free, Available for download, Freely available | biotools:blobtools | https://github.com/DRL/blobtools, https://bio.tools/blobtools | SCR_017618 | BlobTools | 2026-08-13 09:30:04 | 225 | |||||
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VisuAlign Resource Report Resource Website 10+ mentions |
VisuAlign (RRID:SCR_017978) | data analysis software, data processing software, software application, image analysis software, software resource, registration software | Software tool for applying user guided nonlinear refinements (inplane) to existing, affine 2D-to-3D registration. Used for precise quantitative analysis of residual anatomical variability among test subjects after registration with QuickNII. VisuAlign is part of the QUINT workflow. | Nonlinear refinement, 2D, 3D, registration, quantitative analysis, residual anatomical variability |
is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Nutil - Neuroimaging utilities works with: Waxholm Space |
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). | PMID:41069395 | Free, Available for download, Freely available | https://visualign.readthedocs.io; https://github.com/Tevemadar/VisuAlign, https://github.com/Neural-Systems-at-UIO/VisuAlign | SCR_017978 | 2026-08-13 09:30:15 | 41 | |||||||
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3D DART Resource Report Resource Website 1+ mentions |
3D DART (RRID:SCR_017588) | web application, service resource, software resource | DNA structure modelling server. Web server for generating custom 3D structural models of DNA with control over local and global conformation. | Generating, custom, 3D, structural, model, DNA, conformation | EU ; Netherlands Organization for Scientific Research |
PMID:19417072 | Free, Freely available | SCR_017588 | 3DNA-Driven DNA Analysis and Rebuilding Tool | 2026-08-13 09:30:04 | 1 | ||||||||
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Ngmlr Resource Report Resource Website 10+ mentions |
Ngmlr (RRID:SCR_017620) | NGMLR | data processing software, software application, image analysis software, alignment software, software resource | Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection. | Long, read, mapper, align, PacBio, Oxford Nanopore, read, reference, genome, structural, variantion, detection, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Science Foundation ; NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:ngmlr | https://bio.tools/ngmlr | SCR_017620 | coNvex Gap-cost alignMent for Long Reads | 2026-08-13 09:29:46 | 36 | ||||
|
PatchDock Resource Report Resource Website 100+ mentions |
PatchDock (RRID:SCR_017589) | data access protocol, simulation software, software application, web service, software resource | Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles. | Molecular, docking, structure, prediction, protein, molecule, shape, complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Israel Science Foundation ; Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University ; Israeli Ministry of Science ; National Cancer Institute ; NIH |
PMID:15980490 | Free, Freely available | biotools:patchdock | https://bio.tools/patchdock | SCR_017589 | 2026-08-13 09:29:45 | 104 | ||||||
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Rayyan QCRI Resource Report Resource Website 100+ mentions |
Rayyan QCRI (RRID:SCR_017584) | web application, mobile app, software resource, software application | Software tool for screening papers for systematic reviews. Web and mobile app to help to expedite initial screening of abstracts and titles using process of semi automation while incorporating high level of usability. | Screening, paper, systematic, review, abstract, title, process, semi, automation | DOI:10.1186/s13643-016-0384-4 | SCR_017584 | 2026-08-13 09:29:45 | 109 | |||||||||||
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LAN toolbox Resource Report Resource Website 1+ mentions |
LAN toolbox (RRID:SCR_017629) | LANtoolbox | data analysis software, data processing software, software application, software toolkit, time-series analysis software, 1d time-series analysis software, software resource | Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB. | Neuroscientist, data, EEG, experimental, analysis, code, script | is related to: MATLAB | Free, Available for download, Freely available | SCR_017629 | Laboratory of Analysis in Neurosciences Toolbox, EEG Toolbox | 2026-08-13 09:30:04 | 2 | ||||||||
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Macquarie University; Sydney; Australia Resource Report Resource Website 1+ mentions |
Macquarie University; Sydney; Australia (RRID:SCR_017596) | topical portal, data or information resource, portal | Public research university based in Sydney, Australia, in suburb of Macquarie Park. Founded in 1964 by New South Wales Government, it was third university to be established in metropolitan area of Sydney. | SCR_017596 | 2026-08-13 09:30:04 | 8 | |||||||||||||
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ToupView Resource Report Resource Website 10+ mentions |
ToupView (RRID:SCR_017998) | data processing software, software application, image acquisition software, data acquisition software, software resource, image processing software | Software tool that controls microscope camera by Touptek Photomics. Provides functions to fully control camera and present video stream processed by Ultra FineTM color engine at high speed, which includes dedicated pipeline to process raw data into realistic scene. Compatible with ToupCam full series of digital cameras. With authorized license, ToupView software could be used with other cameras which support Twain or DirectShow interface. Used in field of medical microscopic imaging, industrial detection, machine vision, astronomical observation, etc. | Control, microscope, camera, Touptek Photomics, video stream, raw data, imaging | Restricted | SCR_017998 | 2026-08-13 09:29:56 | 13 | |||||||||||
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BioAssay Express Resource Report Resource Website 1+ mentions |
BioAssay Express (RRID:SCR_017594) | data access protocol, software resource, service resource, web service | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | 2026-08-13 09:30:04 | 1 | |||||||
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Biotite Resource Report Resource Website 1+ mentions |
Biotite (RRID:SCR_017593) | data analysis software, data processing software, software application, software toolkit, data visualization software, service resource, software resource | Software Python package bundling popular tasks in computational molecular biology, from sequence analysis to structural bioinformatics. Comprehensive library for computational molecular biology. Package features sequence and structure data analysis and editing functionality, support for common sequence and structure file formats, visualization capabilities, interfaces to external software (MSA software, BLAST, DSSP). Operating system(s): Windows, OS X, Linux. | works with: Entrez | DOI:10.1186/s12859-018-2367-z | Free, Available for download, Freely available | SCR_017593 | 2026-08-13 09:30:04 | 5 | ||||||||||
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Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | workflow software, data processing software, software resource, software application | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 81573023 ; National Key Research and Development Program 2017YFC0908500 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-08-13 09:29:57 | 2 | |||||
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syGlass Resource Report Resource Website 10+ mentions |
syGlass (RRID:SCR_017961) | data analysis software, data processing software, software application, data visualization software, software resource | Software visualization tool for direct volume rendering with no segmentation required. Enables users to view, annotate and analyze 3D data in VR. Data visualization and annotation system that allows rendering of large, volumetric data in its true, three- or four-dimensional form. | Direct, volume, rendering, no segmentation, view, analyze, annotate, 3D, data, large, volumetric, IstoVisio, Inc | Commercially available | SCR_017961 | 2026-08-13 09:30:08 | 16 | |||||||||||
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Transcriptomics Explorer Resource Report Resource Website 100+ mentions |
Transcriptomics Explorer (RRID:SCR_017567) | data analysis software, data processing software, software application, data visualization software, service resource, software resource | Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus. | Visualize, analyze, transcriptomic, data, cell, type, mouse, human, Allen, database, multiple, cortical, area, cortex, hippocampus | works with: Allen Brain Atlas | Free, Freely available | https://celltypes.brain-map.org/rnaseq/human/cortex, https://celltypes.brain-map.org/rnaseq/mouse/cortex-and-hippocampus, | SCR_017567 | 2026-08-13 09:30:03 | 108 |
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