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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
VISTA Browser Resource Report Resource Website 50+ mentions |
VISTA Browser (RRID:SCR_011808) | software toolkit, software resource | Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. | Comparative genomics tools, genomic sequences, comparative analysis, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
Office of Biological and Environmental Research ; Office of Science ; US Department of Energy ; NHLBI |
PMID:15215394 | Free, Freely available | OMICS_00948, biotools:vista | http://genome.lbl.gov/vista/index.shtml, https://bio.tools/vista | SCR_011808 | VISTA, vista | 2026-08-02 09:06:03 | 87 | |||||
|
MultiQC Resource Report Resource Website 1000+ mentions |
MultiQC (RRID:SCR_014982) | data access protocol, software resource | Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python. | bioinformatics, data aggregate, python, open source, html report, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Science for Life Laboratory ; National Genomics Infrastructure |
PMID:27312411 DOI:10.1093/bioinformatics/btw354 |
Open source, Available for download | biotools:multiqc, OMICS_12426 | https://github.com/ewels/MultiQC https://pypi.python.org/pypi/multiqc, https://bio.tools/multiqc, https://sources.debian.org/src/multiqc/ | SCR_014982 | 2026-08-02 09:07:05 | 3098 | ||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software toolkit, software resource | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-08-02 09:06:40 | 2839 | ||||||||
|
DANPOS2 Resource Report Resource Website 100+ mentions |
DANPOS2 (RRID:SCR_015527) | software toolkit, software resource | Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing. | nucleosome analysis, protein analysis, protein occupancy, bio.tools |
uses: Dpos is listed by: bio.tools is listed by: Debian |
Available for download, Different versions are available for download | biotools:danpos | https://bio.tools/danpos | SCR_015527 | DANPOS | 2026-08-02 09:06:57 | 111 | |||||||
|
HASTE-project Resource Report Resource Website 1+ mentions |
HASTE-project (RRID:SCR_020932) | software toolkit, software resource | Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data. | Intelligent data pipelines development, intelligent spatial hierarchies, temporal information hierarchies, distributing data, data streams, image data hierarchical approach, image data, hierarchical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:haste_toolkit | https://bio.tools/haste_toolkit | SCR_020932 | HASTE Toolkit, Hierarchical Analysis of Spatial and TEmporal data, Hierarchical Analysis of Spatial and Temporal Data | 2026-08-02 09:08:01 | 1 | |||||||
|
MERMAID Resource Report Resource Website |
MERMAID (RRID:SCR_020939) | software toolkit, software resource | Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures. | Image registration, nonparametric registration, rapid prototyping, new image registration, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Jupyter Notebook |
Free, Available for download, Freely available | biotools:MERMAID | https://github.com/uncbiag/mermaid/blob/master/docs/source/index.rst, https://bio.tools/MERMAID | SCR_020939 | iMagE Registration via autoMAtIc Differentiation | 2026-08-02 09:08:01 | 0 | |||||||
|
scVelo Resource Report Resource Website 100+ mentions |
scVelo (RRID:SCR_018168) | software toolkit, software resource | Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling. | RNA veloscity, analysis, single cell, dynamic modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:scVelo | https://scvelo.readthedocs.io/, https://bio.tools/scVelo | SCR_018168 | scvelo, single-cell RNA Velocity generalized to transient cell states | 2026-08-02 09:07:46 | 199 | |||||||
|
GTDB-Tk Resource Report Resource Website 50+ mentions |
GTDB-Tk (RRID:SCR_019136) | software toolkit, software resource | Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes. | Assigning objective taxonomic classifications, bacterial genome, archaeal genome, Genome Database Taxonomy, metagenome assembled genome, environmental sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:GtDb-tk | https://bio.tools/GTDB-Tk | SCR_019136 | GTDB-Tk v1.3.0, Genome Database Taxonomy-Tk | 2026-08-02 09:07:57 | 79 | |||||||
|
ensembldb Resource Report Resource Website 10+ mentions |
ensembldb (RRID:SCR_019103) | software toolkit, software resource | Software R package to create and use Ensembl based annotation resources. | Ensembl based annotation, Ensembl, annotation, create annotation, use annotation, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:30689724 | Free, Available for download, Freely available | biotools:ensembldb | https://github.com/jorainer/ensembldb, https://bio.tools/ensembldb | SCR_019103 | ensembldb v2.6.8 | 2026-08-02 09:08:05 | 10 | ||||||
|
clustLasso Resource Report Resource Website 1+ mentions |
clustLasso (RRID:SCR_018820) | software toolkit, software resource | Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach. | Predictive signatures, microbial phenotype, cluster lasso approach, build predictive signature, phenotype, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:clustlasso | https://bio.tools/clustlasso | SCR_018820 | 2026-08-02 09:07:53 | 1 | ||||||||
|
Spot Resource Report Resource Website 100+ mentions |
Spot (RRID:SCR_018915) | software toolkit, software resource | Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions. | Numerical perturbation, reproducibility, numerical differences, operating systems, neuroimaging pipeline stability, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available, Available for download | DOI:10.5281/zenodo.3873219, biotools:spottool | https://bio.tools/spottool | SCR_018915 | Spot: File-based localization of numerical perturbations in data analysis pipelines | 2026-08-02 09:07:54 | 141 | |||||||
|
Genomic Annotation in Livestock for positional candidate LOci Resource Report Resource Website 10+ mentions |
Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) | GALLO | software toolkit, software resource | Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens. | QTLs, multi-omics integration, qtl annotation, gene annotation, datamining, qtl enrichment analysis, livestock, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian has parent organization: University of Guelph; Ontario; Canada |
Free, Freely available | biotools:genomic_annotation_in_livestock_for_positional_candidate_loci_gallo | https://bio.tools/genomic_annotation_in_livestock_for_positional_candidate_loci_gallo | SCR_019212 | 2026-08-02 09:08:06 | 14 | |||||||
|
SMI Services Resource Report Resource Website 1+ mentions |
SMI Services (RRID:SCR_018881) | SMI Services | software toolkit, software resource | Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation. | Database management system, anonymising DICOM files, cataloguing DICOM files, medical image, DICOM medical image, image anonymisation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smi_services | https://bio.tools/smi_services | SCR_018881 | Scottish Medical Imaging Services | 2026-08-02 09:07:53 | 1 | ||||||
|
ML Repo Resource Report Resource Website 1+ mentions |
ML Repo (RRID:SCR_017079) | MLRepo | storage service resource, data repository, service resource | Machine learning repository for microbiome datasets. | machine, learning, repository, microbiome, dataset, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:ML_Repo | https://bio.tools/ML_Repo | SCR_017079 | Machine Learning Repository | 2026-08-04 09:44:04 | 2 | ||||||
|
BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-08-04 09:42:17 | 39 | ||||||
|
SimVascular Resource Report Resource Website 50+ mentions |
SimVascular (RRID:SCR_002686) | software application, simulation software, software resource | Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC. | simulation software, fluid dynamics, blood flow, cardiovascular, image-based geometric modeling, image segmentation, mesh generation, vascular, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Simtk.org |
PMID:31446517 | Free, Available for download, Freely available | nif-0000-23311, BioTools:SimVascular, biotools:SimVascular | https://bio.tools/SimVascular, https://bio.tools/SimVascular, https://bio.tools/SimVascular | SCR_002686 | SimVascular: Cardiovascular Modeling and Simulation | 2026-08-05 10:43:40 | 70 | ||||||
|
NEST Simulator Resource Report Resource Website 100+ mentions |
NEST Simulator (RRID:SCR_002963) | NEST | software application, simulation software, software resource | Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity. | simulation, neuron, spiking, neural network, model, neural system, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MUlti SImulation Coordinator has parent organization: NEST Initiative |
DOI:10.1007/978-1-4614-7320-6_258-5 | Free, Available for download, Freely available | nif-0000-00162, biotools:nest | https://github.com/nest/nest-simulator, https://bio.tools/nest | SCR_002963 | Neural Simulation Tool, NEural Simulation Tool, nest, nest-simulator | 2026-08-05 10:43:43 | 175 | |||||
|
Mammalian Gene Collection Resource Report Resource Website 10+ mentions |
Mammalian Gene Collection (RRID:SCR_007024) | MGC | cell repository, material resource, biomaterial supply resource | NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: ATCC is related to: GenBank is related to: Invitrogen Clones is related to: Open Biosystems is related to: Zebrafish Gene Collection has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | biotools:mammalian_gene_collection, nif-0000-00195 | https://bio.tools/mammalian_gene_collection | SCR_007024 | Mammalian Gene Collection | 2026-08-04 09:41:44 | 46 | |||||
|
MULTIDISEQ Resource Report Resource Website |
MULTIDISEQ (RRID:SCR_009304) | MULTIDISEQ | software application, software resource | A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154494, biotools:multidiseq | https://bio.tools/multidiseq | SCR_009304 | 2026-08-04 09:42:20 | 0 | ||||||||
|
MPDA Resource Report Resource Website 10+ mentions |
MPDA (RRID:SCR_009303) | MPDA | software application, software resource | A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, matlabr, ms-windows, (windows98/2000/xp), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:mpda, nlx_154492 | https://bio.tools/mpda | SCR_009303 | Microarray Pooled DNA Analyser | 2026-08-04 09:42:21 | 12 |
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