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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pyntacle Resource Report Resource Website 1+ mentions |
Pyntacle (RRID:SCR_019030) | software resource, network analysis software, data analysis software, data processing software, software application | Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools. | Graph analysis, topology, group centrality, systems biology, parallel computing, data conversion tool, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:pyntacle | https://bio.tools/pyntacle | SCR_019030 | 2026-08-06 09:29:30 | 1 | ||||||||
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StoatyDive Resource Report Resource Website 1+ mentions |
StoatyDive (RRID:SCR_018796) | data analysis software, software application, software resource, data processing software | Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. | Evaluate predicted peak profile, classify predicted peak profile, assess binding specificity, protein-target specificity, sequencing data, CLIP-seq data, CHIP-Seq data, peak profile data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | SCR_018800, biotools:StoatyDive | https://bio.tools/StoatyDive | SCR_018796 | 2026-08-06 09:29:22 | 1 | ||||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, software application, software resource, data processing software | 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 | 2026-08-06 09:29:23 | 3 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | software resource, data analysis software, data processing software, data visualization software, software application | 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 | 2026-08-06 09:29:30 | 1 | ||||||||
|
Seqtk Resource Report Resource Website 500+ mentions |
Seqtk (RRID:SCR_018927) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software fast and lightweight tool for processing sequences in FASTA or FASTQ format. | Sequence processing, FASTA format, FASTQ format, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_09736, biotools:seqtk | https://bio.tools/seqtk, https://sources.debian.org/src/seqtk/ | SCR_018927 | SEQTK | 2026-08-06 09:29:23 | 827 | |||||||
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CopyDetective Resource Report Resource Website 1+ mentions |
CopyDetective (RRID:SCR_018909) | software resource, algorithm resource, data analysis software, data processing software, software application | Software tool for detection threshold aware CNV calling in matched whole exome sequencing data. | Copy number variant calling, whole exome sequencing data, detection thresholds, deletion, duplication, case control samples, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Munster; North Rhine-Westphalia; Germany |
EU 634789 (Horizon2020 MDS-RIGHT); DFG TU 298/5-1 (DFG Clinical Research Unit 326 Male Germ Cells: from Genes to Function); DKH 111347; Löwenkinder - Verein zur Unterstützung krebskranker Kinder e.V. ; DKS DKS349 2014.11 A/B (NHL-BFM Registry 2012) |
Free, Available for download, Freely available | biotools:copydetective | https://bio.tools/copydetective | SCR_018909 | 2026-08-06 09:29:24 | 1 | |||||||
|
GEMB Resource Report Resource Website 1+ mentions |
GEMB (RRID:SCR_018904) | data analysis software, software application, software resource, data processing software | Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function. | Gene set enrichement, mathematical biology, disease and gene association, biophysical property, gene perturbation prediction, weighted gene set test, recover p-value, bio.tools |
uses: MATLAB is listed by: bio.tools is listed by: Debian |
DOI:10.1101/554212 | Free, Freely available | biotools:gemb | https://bio.tools/gemb | SCR_018904 | Gene Set Enrichment for Mathematical Biology | 2026-08-06 09:29:29 | 1 | ||||||
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DicomTypeTranslator Resource Report Resource Website 1+ mentions |
DicomTypeTranslator (RRID:SCR_018878) | data management software, software application, software resource | Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database. | DICOM SQL conversion, DICOM file, metadata extraction, SQL database, indexing and storage, file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:dicomtypetranslation | https://bio.tools/dicomtypetranslation | SCR_018878 | 2026-08-06 09:29:22 | 1 | ||||||||
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RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, software application, software resource, data processing software | 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 | 2026-08-06 09:29:29 | 8 | ||||||
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GEDIT Resource Report Resource Website 10+ mentions |
GEDIT (RRID:SCR_019277) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices. | bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/728493 | Free, Freely available | biotools:gedit | http://webtools.mcdb.ucla.edu/, https://bio.tools/gedit | SCR_019277 | Gene Expression Deconvolution Interactive Tool | 2026-08-06 09:29:27 | 12 | ||||||
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SoupX Resource Report Resource Website 50+ mentions |
SoupX (RRID:SCR_019193) | software resource, data analysis software, software toolkit, data processing software, software application | Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. | Estimation, removal, cell free mRNA contamination, droplet based, single cell RNA-seq data, RNA-seq data, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:soupx | https://bio.tools/soupx | SCR_019193 | 2026-08-06 09:29:29 | 77 | ||||||||
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tradeSeq Resource Report Resource Website 10+ mentions |
tradeSeq (RRID:SCR_019238) | data analysis software, software application, software resource, data processing software | Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data. | Dynamic temporal gene regulation, gene regulation identifying, gene regulation, single cell RNA-seq data, differential expression analysis, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tradeseq | https://bioconductor.org/packages/tradeSeq/, https://bio.tools/tradeseq | SCR_019238 | TRAjectory-based Differential Expression analysis for SEQuencing data | 2026-08-06 09:29:30 | 35 | |||||||
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ShinyGO Resource Report Resource Website 500+ mentions |
ShinyGO (RRID:SCR_019213) | data access protocol, web service, software resource | Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks. | Graphical gene set enrichment, animal gene, plant gene, graphical visualization, enrichment results, gene characteristics, pathway diagrams retrieval, protein interaction network, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: STRING is related to: KEGG has parent organization: South Dakota State University; South Dakota; USA |
PMID:31882993 | biotools:ShinyGO | https://bio.tools/ShinyGO | SCR_019213 | ShinyGO 0.77, ShinyGO 0.80, Shiny Gene Ontology, ShinyGO v0.61 | 2026-08-06 09:29:32 | 842 | |||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, software application, software resource, data processing software | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-08-06 09:29:26 | 2638 | ||||||
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D-EE Resource Report Resource Website 1+ mentions |
D-EE (RRID:SCR_019058) | software resource, data analysis software, data processing software, data visualization software, software application | Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup. | Distributed dimensionality reduction, dimensionality reduction, distributed storage, distributed computation, large scale data, single cell data, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:d-ee | https://bio.tools/d-ee | SCR_019058 | 2026-08-06 09:29:31 | 1 | ||||||||
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eMouseAtlas Resource Report Resource Website 50+ mentions |
eMouseAtlas (RRID:SCR_002981) | EMAP, EMA, EMAGE, MAP, EMAP, MAP2.0, | database, data or information resource, atlas | Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped. | Mouse Atlas Project, molecular neuroanatomy resource, adult mouse, mouse, brain, c57bl/6j, magnetic resonance microscopy, diffusion-weighted image, blockface imaging, immunohistochemistry, in situ hybridization, neuroanatomy, mri, dti, brain architecture, gene expression, neuroimaging, ontology, connectivity, histology, neuronal tract tracing, genetic labeling, newborn mouse, experimental protocol, bio.tools, ontology, histology, mouse embryo, gene expression, gxd query interface, digital anatomical atlas, spatial region, domain, 2d, 3d, virtual embryo model, development atlas, standard anatomical nomenclature, developmental staging criteria, spatially mapped, anatomy nomenclature, molecular neuroanatomy resource, embryonic mouse, FASEB list |
is related to: GUDMAP Ontology is related to: EMAGE Gene Expression Database is related to: EMAGE Gene Expression Database is related to: HUDSEN is related to: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: Jackson Laboratory is parent organization of: Minimal Anatomical Terminology |
Medical Research Council ; NINDS ; NIBIB ; NIDA ; NIDCD ; NIA |
PMID:15043218 PMID:18077470 PMID:16381949 |
Free, Freely available | nif-0000-00038, nif-0000-00505, biotools:emap, biotools:ma, SCR_007281 | http://www.emouseatlas.org/emap/home.html, https://bio.tools/emap, https://bio.tools/ma | http://genex.hgu.mrc.ac.uk/, http://www.loni.ucla.edu/MAP/ | SCR_002981 | emouseatlas, e-mouse Atlas, EMAGE Gene Expression Database, EMA, Edinburgh Mouse Atlas of Gene Expression, e-Mouse Atlas, EMA Anatomy Atlas of Mouse Development | 2026-08-06 09:25:46 | 69 | |||
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ResponseNet Resource Report Resource Website 1+ mentions |
ResponseNet (RRID:SCR_003176) | ResponseNet | data analysis service, production service resource, analysis service resource, service resource | WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming. | interactome, gene, protein, signaling pathway, signaling, regulatory, pathway, regulatory pathway, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23761447 PMID:21576238 |
Free, Freely available | biotools:responsenet, OMICS_01562 | https://bio.tools/responsenet | http://netbio.bgu.ac.il/respnet/ | SCR_003176 | 2026-08-06 09:25:49 | 4 | |||||
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IntEnz- Integrated relational Enzyme database Resource Report Resource Website 10+ mentions |
IntEnz- Integrated relational Enzyme database (RRID:SCR_002992) | IntEnz | database, data or information resource | IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. | enzyme categories, enzyme classification, enzyme nomenclature, enzyme reaction categories, enzyme, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: ENZYME has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics |
European Union SLING 226073 | PMID:14681451 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03028, biotools:intenz, r3d100010803 | https://bio.tools/intenz | SCR_002992 | 2026-08-06 09:25:46 | 13 | |||||
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PILGRM Resource Report Resource Website 1+ mentions |
PILGRM (RRID:SCR_004749) | PILGRIM | data analysis service, production service resource, analysis service resource, service resource | PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis. | data mining, gene expression, user directed data mining, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NIGMS P50 GM071508; NCI T32 CA005928 |
PMID:21653547 | nlx_75372, biotools:pilgrm | https://bio.tools/pilgrm | SCR_004749 | Platform for Interactive Learning by Genomics Results Mining | 2026-08-06 09:26:13 | 1 | |||||
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HSSP Resource Report Resource Website 10+ mentions |
HSSP (RRID:SCR_004953) | HSSP | database, data or information resource | HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. Homologues are very likely to have the same 3D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of sequence aligned sequence families, but it is also a database of implied secondary and tertiary structures. Likely secondary structure are carried over from the PDB protein to each homologous protein. Tertiary structure models can be built by fitting the sequence of the homologue as aligned into the 3D template of the protein of known structure. Special software is needed to construct 3D models by homology, such WHATIF by Gert Vriend or MaxSprout by Liisa Holm and Chris Sander. The command rsync can be used to obtain a local copy of the HSSP. We appreciate receiving an Email from people who do so, but there are no strings attached. Everybody can freely download the files, academia and industry alike. If your institute''s firewall doesn''t allow you to use the (preferred) rsync way of obtaining HSSP files, feel free to work with FTP. The files are in that case available from: ftp://ftp.cmbi.ru.nl//pub/molbio/data/hssp/ | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:2017436 | biotools:hssp, nlx_91976 | https://bio.tools/hssp | SCR_004953 | Homology-derived Secondary Structure of Proteins, homology-derived structures of proteins, HSSP - Homology derived Secondary Structure of Proteins, HSSP database, HSSP - Homology-derived Secondary Structure of Proteins, Homology derived Secondary Structure of Proteins | 2026-08-06 09:26:15 | 33 |
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