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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | SciCrunch Registry | 2026-09-26 02:19:28 | 1908 | ||||||
|
PhyML Resource Report Resource Website 5000+ mentions |
PhyML (RRID:SCR_014629) | software resource, source code, web application | Web phylogeny server based on the maximum-likelihood principle. | phylogenic software, phylogeny, maximum likelihood, web server, bio.tools |
is used by: ProtTest is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: PAML |
DOI:10.1093/molbev/msq060 | Public server, Source code is available on request | biotools:phyml, OMICS_04241 | https://bio.tools/phyml, https://sources.debian.org/src/phyml/ | SCR_014629 | SciCrunch Registry | 2026-09-26 02:19:24 | 7951 | |||||||
|
QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | data analytics software, software application, software resource | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool, https://bio.tools/qmrlfs-finder | SCR_014584 | SciCrunch Registry | QmRLFS finder | 2026-09-26 02:19:26 | 16 | |||||
|
FunRich: Functional Enrichment analysis tool Resource Report Resource Website 100+ mentions |
FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) | data analytics software, software application, software resource, standalone software | A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts. | network analysis, background database, charts, data analytics software, standalone software, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:25921073 PMID:26149235 |
Public, Open Source | biotools:funrich | https://bio.tools/funrich | SCR_014467 | SciCrunch Registry | 2026-09-26 02:19:24 | 431 | |||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-09-26 02:19:25 | 3080 | ||||||||
|
Clinotator Resource Report Resource Website 1+ mentions |
Clinotator (RRID:SCR_016054) | software application, software resource | Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics. | clinical, age, weight, score, metric, vcf, python, nbci, annotation, variant, scoring, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free | biotools:clinotator | https://bio.tools/clinotator | SCR_016054 | SciCrunch Registry | clinotator.py | 2026-09-26 02:19:26 | 2 | |||||||
|
DANPOS2 Resource Report Resource Website 100+ mentions |
DANPOS2 (RRID:SCR_015527) | software resource, software toolkit | 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 | SciCrunch Registry | DANPOS | 2026-09-26 02:19:26 | 114 | |||||||
|
PREDDIMER Resource Report Resource Website 10+ mentions |
PREDDIMER (RRID:SCR_011963) | PREDDIMER | analysis service resource, data analysis service, production service resource, service resource | Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24202542 | Free | OMICS_01614, biotools:preddimer | https://bio.tools/preddimer | SCR_011963 | SciCrunch Registry | PREDDIMER - Prediction tool for an ensemble of transmembrane ?-helical dimer conformations | 2026-09-26 02:18:47 | 15 | |||||
|
Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | data or information resource, database | Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). | protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Bioinformatics Institute; Singapore; Singapore |
PMID:22139934 | nlx_149432, biotools:cube-db | https://bio.tools/cube-db | SCR_013233 | SciCrunch Registry | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-09-26 02:18:50 | 3 | ||||||
|
Open Trials Resource Report Resource Website 1+ mentions |
Open Trials (RRID:SCR_015570) | data or information resource, database | Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally. | clinical trial, clinical trial database, clinical trial data, open database, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
Laura and John Arnold Foundation ; Wellcome Trust ; World Health Organisation ; West of England Academic Health Science Network |
Open source | biotools:opentrials | https://bio.tools/opentrials | SCR_015570 | SciCrunch Registry | 2026-09-26 02:18:55 | 3 | |||||||
|
Genome Aggregation Database Resource Report Resource Website 5000+ mentions |
Genome Aggregation Database (RRID:SCR_014964) | gnomAD | data or information resource, database | Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. | database, genome, , bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Broad Institute Genomics Platform has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
Broad Institute | Open source, Available to the biomedical community, The community can contribute to this resource | biotools:gnomad | https://github.com/macarthur-lab/gnomad_browser/issues, https://bio.tools/gnomad | SCR_014964 | SciCrunch Registry | gnomAD 2.0, gnomAD Browser, gnomAD version 2.0, Exome Aggregation Consortium | 2026-09-26 02:18:54 | 5310 | |||||
|
lncRNAdb Resource Report Resource Website 100+ mentions |
lncRNAdb (RRID:SCR_015491) | data or information resource, database | Searchable database of comprehensive annotations of eukaryotic long non-coding RNAs. Entries are manually curated from referenced literature. | reference database, eukaryotic annotation, annotation database, eukaryotic long non coding rna database, functional long noncoding rnas, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
Open source, Acknowledgement requested, The community can contribute to this resource | biotools:lncrnadb | https://bio.tools/lncrnadb | SCR_015491 | SciCrunch Registry | lncRNAdb v2.0, Long Noncoding RNA Database, Long Noncoding RNA Database v2.0 | 2026-09-26 02:18:54 | 165 | |||||||
|
UniCarbKB Resource Report Resource Website 10+ mentions |
UniCarbKB (RRID:SCR_014410) | data or information resource, database | International effort which has created a glycomics knowledgebase with access to a database of information on the glycan structures of glycoproteins. It serves as and promotes an online information storage and search platform for glycomics and glycobiology research. Open access knowledgebase offers resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data. | knowledgebase, glycomics, glycerin structure, glycoprotein, cell line, glycoproteomics knowledge platform, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Macquarie University; Sydney; Australia has parent organization: University of Gothenburg; Gothenburg; Sweden has parent organization: SIB Swiss Institute of Bioinformatics is parent organization of: UniCarb-DB |
DOI:10.1093/nar/gkt1128 | Free, Freely available | biotools:unicarbkb | https://bio.tools/unicarbkb | http://www.unicarbkb.org | SCR_014410 | SciCrunch Registry | 2026-09-26 02:18:53 | 28 | ||||||
|
SnpSift Resource Report Resource Website 500+ mentions |
SnpSift (RRID:SCR_015624) | software resource, software toolkit, source code | Software toolkit for filtering and manipulating annotated files. After annotation, the software's filter function can find relevant genomic variants in large data files. | annotation, filtering, genomic variant, single nucleotide polymorphism, bio.tools |
is listed by: bio.tools is listed by: Debian works with: SnpEff |
PMID:22728672 | Open Source, Free, Available for download | biotools:snpsift | https://bio.tools/snpsift | SCR_015624 | SciCrunch Registry | SnpEff | 2026-09-26 02:18:55 | 631 | ||||||
|
ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | data or information resource, database | An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data | cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools |
uses: SynView is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:16381902 | nif-0000-02698, biotools:cryptodb, r3d100012265 | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | SciCrunch Registry | CryptoDB, Cryptosporidium Genomics Resource | 2026-09-26 02:18:51 | 26 | ||||
|
Examl Resource Report Resource Website 50+ mentions |
Examl (RRID:SCR_016087) | Examl | software application, software resource, source code | Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers. | phylogenetic, analysis, database, large scale, whole genome, whole transcriptome, alignment, efficiency, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Heidelberg Institute for Theoretical Studies | PMID:25819675 | Free, Available for download | OMICS_08024, biotools:ExaML | https://bio.tools/ExaML, https://sources.debian.org/src/examl/ | SCR_016087 | SciCrunch Registry | Examl:Exascale Maximum Likelihood | 2026-09-26 02:18:55 | 62 | ||||
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ExPASy ABCD database Resource Report Resource Website 10+ mentions |
ExPASy ABCD database (RRID:SCR_017401) | ABCD ExPASy, The ABCD database | data or information resource, database | Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities. Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments. | Sequenced antibody, manually curated, known target, ExPASy, repository, chemically defined antibodies, antibody, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: SIB Swiss Institute of Bioinformatics has parent organization: University of Geneva; Geneva; Switzerland |
ProCare Foundation ; Swiss National Science Foundation ; University of Geneva |
PMID:31410491 | Free, Freely available | SCR_019000, biotools:AbCD_database | https://bio.tools/ABCD_database | SCR_017401 | SciCrunch Registry | ExPASy ABCD (AntiBodies Chemically Defined) Database, The ABCD database, AntiBodies Chemically Defined, AntiBodies Chemically Defined Expert Protein Analysis System database, ExPASy ABCD Database, The AntiBodies Chemically Defined Database | 2026-09-26 02:18:56 | 13 | ||||
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Signaling Pathways Project Resource Report Resource Website 10+ mentions |
Signaling Pathways Project (RRID:SCR_018412) | SPP | data or information resource, database | Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available. | Data integration, genetic database, gene regulatory network, cell signalling, cellular signalling network, transcriptomic data, manualy curated, cistromic data, cellular receptor, enzyme, transcrptomic factor, mammalian cellular signaling pathway, data mining strategy, dataset, , bio.tools |
is used by: Hypothesis Center is listed by: Debian is listed by: bio.tools works with: Gene Expression Omnibus (GEO) works with: NCBI Sequence Read Archive (SRA) |
CPRIT RP150578; Dan L. Duncan NCI Comprehensive Cancer Center at Baylor College of Medicine ; NCI CA125123; NHLBI HL127624; NIDDK DK095686; NIDDK DK097748; NIDDK DK097771; NIDDK DK105126; NIDDK DK107535; NIDDK DK48807; NIDDK DK56338 |
PMID:31672983 | Free, Freely available | r3d100013650, biotools:Signaling_Pathways_Project | https://bio.tools/Signaling_Pathways_Project, https://doi.org/10.17616/R31NJN0Y | https://www.signalingpathways.org | SCR_018412 | SciCrunch Registry | 2026-09-26 02:18:57 | 34 | ||||
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MethBase Resource Report Resource Website 1+ mentions |
MethBase (RRID:SCR_017487) | data or information resource, database, service resource | Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics. | Methylome, database, public, BSseq, dataset, methylation, site, region, allele, specific, metadata, statistics, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
Free, Freely available | BioTools:MethBase, biotools:Methbase | https://bio.tools/MethBase, https://bio.tools/MethBase, https://bio.tools/MethBase | SCR_017487 | SciCrunch Registry | MethBase: a reference methylome database | 2026-09-26 02:18:56 | 1 | |||||||
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VeryFastTree Resource Report Resource Website 1+ mentions |
VeryFastTree (RRID:SCR_023594) | software application, software resource, source code | Software tool for speeding up estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies. | large alignments, phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: bio.tools is related to: FastTree |
ERDF ; MICINN ; Xunta de Galicia |
PMID:32573652 DOI:10.1093/bioinformatics/btaa582 |
Free, Available for download, Freely available | biotools:veryfasttree | https://bio.tools/veryfasttree | SCR_023594 | SciCrunch Registry | 2026-09-26 02:18:59 | 8 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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