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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HUGE - Human Unidentified Gene-Encoded large proteins Resource Report Resource Website 10+ mentions |
HUGE - Human Unidentified Gene-Encoded large proteins (RRID:SCR_013482) | data or information resource, database | The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on. | cdna, human protein, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-02990, biotools:huge | https://bio.tools/huge | SCR_013482 | HUGE | 2026-08-05 10:46:02 | 17 | ||||||||
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KAVIAR Resource Report Resource Website 10+ mentions |
KAVIAR (RRID:SCR_013737) | data or information resource, database | A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants. | SNV, single nucleotide variant, database, indel, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute for Systems Biology; Washington; USA |
Inova Translational Medicine Institute | PMID:21965822 | Free, Public | biotools:kaviar | https://bio.tools/kaviar | SCR_013737 | queryable database of known variants, Known VARiants | 2026-08-05 10:46:03 | 17 | |||||
|
MobiDB Resource Report Resource Website 100+ mentions |
MobiDB (RRID:SCR_014542) | data or information resource, database | A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING. | database, protein disorder, mobility, annotation, intrinsic protein disorder, bio.tools, FASEB list |
uses: UniProt uses: STRING uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Pfam is listed by: bio.tools is listed by: Debian has parent organization: University of Padua; Padua; Italy |
Available to the research community | biotools:mobidb | https://bio.tools/mobidb | SCR_014542 | 2026-08-05 10:46:08 | 130 | ||||||||
|
Research-tested Intervention Programs (RTIPs) Resource Report Resource Website 10+ mentions |
Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) | RTIPs | data or information resource, database | Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials. | cancer, control, intervention, prevention, diagnosis, planning, research, program, public, health, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
cancer | NCI | Freely available, Public | biotools:rtips | https://bio.tools/rtips | SCR_016042 | Research-tested Intervention Programs | 2026-08-05 10:46:31 | 25 | ||||
|
3D-footprint Resource Report Resource Website |
3D-footprint (RRID:SCR_015713) | data or information resource, database | Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats. | dna binding protein structure, protein data bank, sequencing, protein-dna interface, bio.tools |
is listed by: Debian is listed by: bio.tools works with: footprintDB |
CSIC 200720I038 | PMID:19767616 | Freely available, Free for academic use, Tutorial available | biotools:3d-footprint | https://bio.tools/3d-footprint | SCR_015713 | 2026-08-05 10:46:27 | 0 | ||||||
|
ProteomicsDB Resource Report Resource Website 100+ mentions |
ProteomicsDB (RRID:SCR_015562) | data or information resource, database | Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository. | human proteome, human proteomics, proteomics database, human proteomics database, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ProteomeTools has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:24870543 | The research community can contribute to this resource | r3d100013408, biotools:proteomicsdb | https://bio.tools/proteomicsdb, https://doi.org/10.17616/R31NJMU8 | SCR_015562 | 2026-08-05 10:46:25 | 149 | |||||||
|
EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | software toolkit, source code, software resource | Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. | gene set, rna sequencing, analysis method, r package, bio.tools |
is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
Victorian State Government Operational Infrastructure Support ; Australian Government NHMRC IRIISS ; NHMRC GNT1050661; NHMRC GNT1045936; NHMRC GNT1057854; NHMRC GNT1104924 |
PMID:27694195 | Free, Available for download | biotools:egsea | https://bio.tools/egsea | SCR_015036 | Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses | 2026-08-05 10:46:15 | 62 | |||||
|
Embassy-domsearch Resource Report Resource Website |
Embassy-domsearch (RRID:SCR_016086) | software toolkit, source code, software resource | Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. | dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology |
is used by: RAVEN is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/embassy-domsearch/ | SCR_016086 | 2026-08-05 10:46:32 | 0 | |||||||||
|
Datasets2Tools Resource Report Resource Website 1+ mentions |
Datasets2Tools (RRID:SCR_016174) | data or information resource, database | Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools. | biomedical, digital, bioinformatics, dataset, rna seq, computation, microarray, proteomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Public, Freely available | biotools:datasets2tools | https://bio.tools/datasets2tools | SCR_016174 | 2026-08-05 10:46:33 | 1 | ||||||||
|
cwltool Resource Report Resource Website 10+ mentions |
cwltool (RRID:SCR_015528) | software toolkit, source code, software resource | Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host. | language, reference implementation, python |
uses: Python Programming Language is listed by: Debian is listed by: OMICtools |
DOI:10.6084/m9.figshare.3115156.v2 | Available for download | OMICS_28977 | https://sources.debian.org/src/cwltool/ | SCR_015528 | CWLtool, Common Workflow Language Tool | 2026-08-05 10:46:24 | 24 | ||||||
|
TransmiR Resource Report Resource Website 50+ mentions |
TransmiR (RRID:SCR_017499) | data or information resource, database | Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data. | Transcription, factor, miRNA, regulation, manually, curated, TF-miRNA, ChIPseq, derived, TF-miRNA, data, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
Restricted | biotools:transmir | https://bio.tools/transmir/ | SCR_017499 | TransmiR v2.0 | 2026-08-05 10:46:48 | 90 | |||||||
|
HmtVar Resource Report Resource Website 10+ mentions |
HmtVar (RRID:SCR_017288) | data or information resource, service resource, database | Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. | manually, curated, data, variability, mitochondria, pathogenicity, mtDNA, variant, human, bio.tools |
uses: HmtDB - Human Mitochondrial DataBase uses: 1000 Genomes Project and AWS uses: MITOMAP - A human mitochondrial genome database uses: MutPred uses: SNPsandGO is listed by: Debian is listed by: bio.tools is affiliated with: University of Bologna; Bologna; Italy has parent organization: University of Bari; Bari; Italy |
Rosa Maria Massari fellowship from the Italian Association for Cancer Research ; DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-08-05 10:46:53 | 10 | ||||||
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Blood Exposome Database Resource Report Resource Website 1+ mentions |
Blood Exposome Database (RRID:SCR_017610) | data or information resource, database | Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields. | Chemical, compound, collection, extracted, text, mining, PubMed chemical compounds list, PubChem chemical compounds list, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Davis; California; USA |
NIAID U54 AI138370; NIA U19 AG023122; NIEHS U2C ES030158 |
PMID:31557052 | Free, Available for download, Freely available | biotools:blood-exposome-db | https://github.com/barupal/exposome, https://bio.tools/blood-exposome-db | SCR_017610 | The Blood Exposome Database, exposome | 2026-08-05 10:46:52 | 7 | |||||
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Populations Resource Report Resource Website |
Populations (RRID:SCR_024175) | software toolkit, software library, software resource | Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions. | Population genetic, individuals or populations distances, allelic frequencies, phylogenetic trees, file conversions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29592 | https://sources.debian.org/src/populations/ | SCR_024175 | populations | 2026-08-05 10:47:59 | 0 | |||||||
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quicktree Resource Report Resource Website 10+ mentions |
quicktree (RRID:SCR_024205) | software toolkit, software library, software resource | Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments. | Neighbor-Joining algorithm, reconstructing phylogenies from huge alignments, | is listed by: Debian | PMID:3447015 | Free, Available for download, Freely available, | https://sources.debian.org/src/quicktree/ | SCR_024205 | 2026-08-05 10:47:59 | 12 | ||||||||
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pycoqc Resource Report Resource Website 10+ mentions |
pycoqc (RRID:SCR_024185) | software toolkit, software resource | Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data. | compute metrics, generate interactive QC plots, Oxford Nanopore technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pycoqc/ | SCR_024185 | 2026-08-05 10:47:59 | 18 | |||||||||
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python-airr Resource Report Resource Website |
python-airr (RRID:SCR_024187) | software toolkit, software library, software resource | Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation. | airr reference library, functions and classes for interacting with AIRR Community Data Representation Standards, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-airr/ | SCR_024187 | 2026-08-05 10:48:00 | 0 | |||||||||
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annotate Resource Report Resource Website |
annotate (RRID:SCR_024221) | software toolkit, software resource | Software R package for using R enviroments for annotation. | R enviroments, annotation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-annotate/ | SCR_024221 | 2026-08-05 10:48:00 | 0 | |||||||||
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affyio Resource Report Resource Website |
affyio (RRID:SCR_024223) | software toolkit, software library, software resource | Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats. | parsing Affymetrix data files, accessing CEL and CDF file formats, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29381 | https://sources.debian.org/src/r-bioc-affyio/ | SCR_024223 | 2026-08-05 10:48:00 | 0 | ||||||||
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altcdfenvs Resource Report Resource Website |
altcdfenvs (RRID:SCR_024225) | software toolkit, software resource | Software R package contains convenience data structures and functions to handle cdfenvs. | convenience data structures and functions, handle cdfenvs, | is listed by: Debian | PMID:15310390 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-altcdfenvs/ | SCR_024225 | alternative CDF environments | 2026-08-05 10:48:00 | 0 |
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