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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | storage service resource, data or information resource, topical portal, disease-related portal, database, service resource, portal, data repository | EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | COVID-19, COVID-19 data, sequence, expression, protein sequence, protein structure, proteome, translatome, analysis, EMBL-EBI | is related to: EMBL-EBI Pathogens - COVID-19 | COVID-19 | Free, Freely available | SCR_018816 | https://www.covid19dataportal.org/ https://www.ebi.ac.uk/about/news/press-releases/embl-ebi-launches-covid-19-data-portal |
SCR_018337 | EMBL-EBI COVID-19 Data Portal, COVID-19 Data Portal | 2026-02-17 10:03:04 | 10 | ||||||
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Cytosplore Viewer Resource Report Resource Website 10+ mentions |
Cytosplore Viewer (RRID:SCR_018330) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Web based interactive visual analysis system for exploration of single cell data published in Allen Cell Types Database and for number of single cell data resources of Brain Initiative Single Cell Network. Allows interactive exploration of hierarchies of cell types, visualization of transcriptome wide gene expression in combination with metadata of individual cells, performing differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout cellular hierarchy and more. | BICCN, visualization, transcriptomics, single cell data, gene expression, metadata, analysis, statistic, cellular hierarchy, Cytosplore |
uses: Allen Cell Types Database is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is related to: Allen Institute for Brain Science is related to: Leiden University; Leiden; Netherlands |
Free, Available for download, Freely available | SCR_018330 | 2026-02-17 10:03:44 | 17 | ||||||||||
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MOLEonline Resource Report Resource Website 10+ mentions |
MOLEonline (RRID:SCR_018314) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features. | biomacromolecular channel, analysis, biomacromolecular pore, biomacromolecular tunnel, transmembrane pore analysis, analysis, biomacromolecular sturcture, physicochemical feature |
works with: PDBe - Protein Data Bank in Europe works with: CSA - Catalytic Site Atlas works with: UniProt |
PMID:29718451 | Free, Freely available | https://mole.upol.cz/online/ | http://old.mole.upol.cz/ | SCR_018314 | MOLEonline 2.0 | 2026-02-17 10:03:44 | 30 | ||||||
|
Proteomic Data Commons Resource Report Resource Website 50+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | storage service resource, data or information resource, production service resource, analysis service resource, database, service resource, data repository | Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication. | Cancer, proteomic, data, precision medicine, diagnosis, treatment, analysis, biospeciment, clinical data, metadata |
is related to: Cancer Research Data Commons has parent organization: National Cancer Institute |
cancer | Restricted | SCR_018273 | 2026-02-17 10:03:03 | 66 | ||||||||
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Interactive Repeated Experiments Dotplot Resource Report Resource Website |
Interactive Repeated Experiments Dotplot (RRID:SCR_018328) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments. | Interactive graphic, repeated independent experiment, repeated experiment data, graph, analysis, dot plot | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018328 | 2026-02-17 10:03:47 | 0 | |||||||||
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Watchdog Resource Report Resource Website 1+ mentions |
Watchdog (RRID:SCR_018355) | data management software, software application, data processing software, data analysis software, software resource | Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent. | Workflow management system, automated data analysis, next generation sequencing, large scale experimental data, analysis | Free, Available for download, Freely available | https://github.com/klugem/watchdog https://anaconda.org/bioconda/watchdog-wms |
SCR_018355 | 2026-02-17 10:03:47 | 2 | ||||||||||
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Big Data Processor Resource Report Resource Website 1+ mentions |
Big Data Processor (RRID:SCR_018484) | BDP | software application, image processing software, data processing software, software resource, image analysis software | Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy. | Image, image processor, data processor, data, processing, analysis, image data, microscopy | is a plug in for: Fiji | Free, Available for download, Freely available | https://github.com/embl-cba/fiji-plugin-bigDataProcessor | SCR_018484 | 2026-02-17 10:03:48 | 2 | ||||||||
|
Harmony Resource Report Resource Website 10+ mentions |
Harmony (RRID:SCR_018809) | software application, data processing software, data acquisition software, image acquisition software, software resource, image analysis software | Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems. | Imaging, analysis, cellular phenotype quantification, PerkinElmer, high content, screening system, cell phenotypic screening, live cell imaging, | is related to: Operetta CLS | Restricted | SCR_018809 | Harmony 4.8 | 2026-02-17 10:03:32 | 29 | |||||||||
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RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, software application, data processing software, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIGMS R01 GM104962; Berlin Institute for Medical Systems Biology |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html https://bio.tools/ribotaper |
SCR_018880 | 2026-02-17 10:03:49 | 8 | ||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, software application, data processing software, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-02-17 10:03:53 | 3 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | software application, data processing software, data analysis software, software resource, data visualization software | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-02-17 10:03:53 | 1 | ||||||||
|
TwoSampleMR Resource Report Resource Website 500+ mentions |
TwoSampleMR (RRID:SCR_019010) | data analysis software, software application, data processing software, software resource | Software R package for performing Mendelian randomization using genome wide association study summary data. | GWAS data, genome wide associated study data, genome data, Mendelian randomization, analysis | PMID:29846171 | Free, Available for download, Freely available | SCR_019010 | 2026-02-17 10:03:51 | 597 | ||||||||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust 206194; Biotechnology and Biological Sciences Research Council BB/M014088/1 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-02-17 10:03:14 | 197 | ||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | alignment software, software application, data processing software, data analysis software, software resource, sequence analysis software, image analysis software | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac https://sources.debian.org/src/atac/ |
SCR_015980 | 2026-02-17 10:02:38 | 1748 | |||||||
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Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/ https://sources.debian.org/src/baitfisher/ |
SCR_015984 | Axe-demultiplexer | 2026-02-17 10:02:56 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data management software, software application, data processing software, data analysis software, software resource, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools https://sources.debian.org/src/bamtools/ |
SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-02-17 10:03:14 | 324 | ||||||
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scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit, data visualization software | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Health and Medical Research Council of Australia APP1112681; European Molecular Biology Laboratory ; Cancer Research UK A17197; United Kingdom Medical Research Council ; Oxford Single Cell Biology Consortium |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/ https://bio.tools/scater |
SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-02-17 10:03:20 | 173 | ||||||
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BIAevaluation Software Resource Report Resource Website 100+ mentions |
BIAevaluation Software (RRID:SCR_015936) | software application, standalone software, data processing software, data analysis software, software resource, data visualization software | Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses. | evaluation, life, science, bia, biacore, sensorgram, bia, analysis, real-time | Commercially Available, Available for purchase, License available for purchase | http://www.molecular-interactions.si/data/equipment/BIAeval3-AC.pdf | SCR_015936 | BIAevaluation Software Kit, BIAevaluation | 2026-02-17 10:03:20 | 457 | |||||||||
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GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data analysis software, software application, data processing software, software resource | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/ https://sources.debian.org/src/garli/ |
SCR_016117 | Genetic Algorithm for Rapid Likelihood Inference | 2026-02-17 10:03:18 | 279 | ||||||
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Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data analysis software, software application, data processing software, software resource | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-02-17 10:03:21 | 15 |
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