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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ClinVar Resource Report Resource Website 5000+ mentions |
ClinVar (RRID:SCR_006169) | ClinVar | storage service resource, service resource, data repository, data or information resource, database | Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard. | sequence variation, variation, phenotype, genetics, genetic variation, clinical, allele, aggregator, geneotype, gene, disease, clinical assertion, bio.tools |
is used by: NIF Data Federation is used by: MARRVEL is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: AutoGVP has parent organization: NCBI |
Free, Freely available | nlx_151671, r3d100013331, biotools:clinvar, OMICS_00262 | https://bio.tools/clinvar, https://doi.org/10.17616/R31NJMS3 | SCR_006169 | 2026-08-06 09:26:31 | 6595 | |||||||
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Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-08-06 09:27:06 | 2 | |||||
|
FragGeneScan Resource Report Resource Website 100+ mentions |
FragGeneScan (RRID:SCR_011929) | sequence analysis software, software resource, data analysis software, data processing software, software application | A software application for finding fragmented genes in short reads and may be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. | microbiome, sequence analysis, fragment, gene, short read, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Acknowledgement requested, Available for download | OMICS_01484, biotools:fraggenescan | http://omics.informatics.indiana.edu/FragGeneScan/, https://bio.tools/fraggenescan | SCR_011929 | 2026-08-06 09:27:51 | 183 | ||||||||
|
Berkeley Advanced Reconstruction Toolbox Resource Report Resource Website 1+ mentions |
Berkeley Advanced Reconstruction Toolbox (RRID:SCR_016168) | BART | software resource, image analysis software, image reconstruction software, data processing software, software application | Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. | mri, reconstruction, magnetic, resonance, neuroimaging, array, transform, algorithm | is listed by: Debian | NCRR R41 RR09784; American Heart Association 12BGIA9660006; NIBIB R01 EB009690; UC Discovery 193037; Sloan Research Fellowship ; GE Healthcare |
Open source, Free | https://mrirecon.github.io/bart/, https://sources.debian.org/src/bart/ | SCR_016168 | 2026-08-06 09:28:46 | 7 | |||||||
|
Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution. | long, read, genome, assembly, hinging, sequence, optimal, repeat, resolution |
is listed by: Debian is listed by: OMICtools |
PMID:28320918 | Free, Available for download | OMICS_12339 | https://sources.debian.org/src/hinge/ | SCR_016135 | 2026-08-06 09:28:48 | 9 | |||||||
|
HH-suite Resource Report Resource Website 10+ mentions |
HH-suite (RRID:SCR_016133) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, software application | Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments. | protein, sensitive sequence search, pairwise alignment, multiple database, homologous structure, prediction, modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
the Deutsche Forschungsgemeinschaft grant SFB646; Ludwig-Maximilians Universität Munich ; Excellence Initiative of the Bundesministerium für Bildung und Forschung |
DOI:10.1186/s12859-019-3019-7 | Free, Available for download, Freely available | biotools:hh-suite | https://bio.tools/hh-suite | http://toolkit.genzentrum.lmu.de/sections/search | SCR_016133 | 2026-08-06 09:28:46 | 49 | |||||
|
DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software resource, software tool, data analysis software, data processing software, software application | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | 2026-08-06 09:28:42 | 43994 | |||||||
|
FreeContact Resource Report Resource Website 10+ mentions |
FreeContact (RRID:SCR_016113) | software resource, image analysis software, alignment software, data processing software, software application | Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud). | protein, structure, prediction, sequence, analysis, fast, contact, alignment, multiple |
is listed by: OMICtools is related to: Debian |
Alexander von Humboldt Foundation ; German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung) ; Research Council of Norway 208481 |
PMID:24669753 DOI:10.1186/1471-2105-15-85 |
Open source, Free, Available for download | OMICS_03520 | https://rostlab.org/owiki/index.php/FreeContact, https://sources.debian.org/src/libfreecontact-perl/ | SCR_016113 | 2026-08-06 09:28:45 | 21 | ||||||
|
Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome. | automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: shovill is hosted by: GitHub |
DOI:10.1371/journal.pone.0112963 DOI:10.1371/journal.pone.0112963 |
Available for download, Acknowledgement requested | OMICS_14553, biotools:pilon | https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ | SCR_014731 | 2026-08-06 09:28:23 | 3102 | |||||||
|
RepeatModeler Resource Report Resource Website 1000+ mentions |
RepeatModeler (RRID:SCR_015027) | sequence analysis software, software resource, data analysis software, data processing software, software application | Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis, sequence repeats, repeat identification, bio.tools |
uses: RepeatScout is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Dfam |
Institute for Systems Biology ; NHGRI R44 HG02244; NHGRI R01 HG002939 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:repeatmodeler | https://bio.tools/repeatmodeler | SCR_015027 | 2026-08-06 09:28:31 | 3193 | |||||||
|
Morpheus Resource Report Resource Website 500+ mentions |
Morpheus (RRID:SCR_014975) | software resource, 3d visualization software, data processing software, data visualization software, software application, simulation software | Modeling and simulation environment for study of multi scale and multicellular systems. Users can construct and simulate models of gene regulation, signaling pathways, tissue patterning and morphogenesis and explore the effects of multiscale feedbacks between these processes. Morpheus can render 2D and 3D models using graphical user interface. | simulation, modeling, multicellular, systems biology, cell-based models, data visualization, differential equations, reaction-diffusion systems, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dresden University of Technology; Saxony; Germany |
BMBF 0315734; BMBF 0316169; DFG |
PMID:24443380 | Free, Available for download, Freely available | biotools:morpheus-framework | https://gitlab.com/morpheus.lab/morpheus, https://bio.tools/morpheus-framework | https://imc.zih.tu-dresden.de/wiki/morpheus | SCR_014975 | 2026-08-06 09:28:31 | 694 | |||||
|
MEBS: Multigenomic Entropy-Based Score Resource Report Resource Website 1+ mentions |
MEBS: Multigenomic Entropy-Based Score (RRID:SCR_015708) | MEBS | data analysis software, software application, software resource, data processing software | Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets. | metagenomics analysis, metabolism, fasta file, protein analysis, omic dataset, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source, Available for download | biotools:mebs | https://bio.tools/mebs | SCR_015708 | metagenome_Pfam_score, Multigenomic Entropy-Based Score, Multigenomic Entropy-Based Score (MEBS) | 2026-08-06 09:28:42 | 1 | ||||||
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RNA FRABASE - RNA FRAgments search engine and dataBASE Resource Report Resource Website |
RNA FRABASE - RNA FRAgments search engine and dataBASE (RRID:SCR_012808) | RNA FRABASE | d spatial image, service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Engine and database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation. The database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types given for the PBD-deposited RNA structures. Knowledge of the three dimensional RNA structure is crucial for all fields of biomolecular research. In contrast to the protein field, only about 1.300 experimentally derived structures of RNAs are deposited in the Protein Data Bank (PDB). To complement the results of experimental studies, new approaches based on bioinformatics and calculation are pursued in several laboratories to make tertiary RNA structure prediction possible. RNA FRABASE version 2.0 should greatly facilitate various RNA structure modelling approaches, RNA structure analysis and motif searching. If one compares the three dimensional RNA structure to a spatial puzzle, the RNA FRABASE allows to pull out a defined piece of this puzzle - the 3D RNA fragment. The architecture of the web-accessible RNA FRABASE engine and database is based on the following information path: PDB-deposited RNA structures �� RNA sequences and secondary structures described in the dot-bracket notation �� secondary structures of RNA fragments �� 3D RNA fragments. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide on the spot structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. | structural element, secondary structure, rna, rna structure, 3d rna fragment, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Polish Academy of Sciences Poznan; Poznan; Poland |
Foundation for Polish Science SP 01/04; Ministry of Education and Science 3T09A014 29; Polish Ministry of Science and Higher Education PBZ-MniSW-07/1/2007/01; Polish Ministry of Science and Higher Education NN 519314635 |
PMID:20459631 PMID:17921499 |
nif-0000-03413, biotools:rna_frabase | https://bio.tools/rna_frabase | SCR_012808 | RNA FRAgments search engine dataBASE, RNA FRAgments search engine and dataBASE, RNA FRABASE - RNA FRAgments search engine dataBASE | 2026-08-06 09:28:04 | 0 | |||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT082930MA; National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882 |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-08-06 09:28:47 | 8 | ||||||
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Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | 2026-08-06 09:29:17 | 602 | ||||||
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | data analysis software, software application, software resource, data processing software | Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. | High density genotyping data, molecular phenotype, gene expression, proteomics, mapping trait loci, diversity outbred mice, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM074244; NIGMS R01 GM070683; NIGMS R01 GM123489 |
PMID:30591514 | Free, Available for download, Freely available | biotools:R_qtl2, SCR_020965 | https://bio.tools/R_qtl2, https://kbroman.org/qtl2, https://github.com/rqtl/qtl2 | SCR_018181 | QTL, R/quantitative trait loci, QTL2, Quantitative Trait Locus 2, quantitative trait loci 2, R/qtl, qtl2 | 2026-08-06 09:29:21 | 13 | |||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-08-06 09:28:53 | 4072 | ||||||
|
CMap Resource Report Resource Website 100+ mentions |
CMap (RRID:SCR_016204) | data set, software resource, data or information resource, web application, database | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-08-06 09:28:46 | 483 | |||||||
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SMARTdenovo Resource Report Resource Website 100+ mentions |
SMARTdenovo (RRID:SCR_017622) | software resource, image analysis software, alignment software, data processing software, software application | Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus. | De novo, assembler, PacBio, Oxford Nanopore, data, sequence, raw, read, alignment, error, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:SMARTdenovo, biotools:SMARtdenovo | https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo | SCR_017622 | 2026-08-06 09:29:07 | 159 | ||||||||
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pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | data acquisition software, software resource, image acquisition software, software toolkit, data processing software, software application | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap, https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf, https://bio.tools/pheatmap, https://sources.debian.org/src/r-cran-pheatmap/ | SCR_016418 | pretty heatmap | 2026-08-06 09:28:49 | 1068 |
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