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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TransmiR Resource Report Resource Website 100+ 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 | 2026-09-03 05:03:46 | 123 | |||||||
|
HmtVar Resource Report Resource Website 10+ mentions |
HmtVar (RRID:SCR_017288) | data or information resource, database, service resource | 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 |
DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health ; Rosa Maria Massari fellowship from the Italian Association for Cancer Research |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-09-03 05:03:18 | 12 | ||||||
|
Blood Exposome Database Resource Report Resource Website 10+ 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 | 2026-09-03 05:03:53 | 11 | |||||
|
MAKER Resource Report Resource Website 1000+ mentions |
MAKER (RRID:SCR_005309) | software resource, software toolkit | Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values. | gene prediction, genome annotation, identifies repeats, aligns ESTs and proteins to genome, data management, genome annotation, annotation, curation, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: MAKER Web Annotation Service has parent organization: University of Utah; Utah; USA |
PMID:25501943 | SCR_023883, nlx_144363, biotools:maker | https://bio.tools/maker, https://github.com/Yandell-Lab/maker | SCR_005309 | Maker2, maker | 2026-09-03 05:04:04 | 1519 | |||||||
|
Unipro UGENE Resource Report Resource Website 100+ mentions |
Unipro UGENE (RRID:SCR_005579) | UGENE | software resource, software toolkit | A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. | c++, windows, mac os, linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22368248 DOI:10.1093/bioinformatics/bts091 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01022, biotools:ugene | https://bio.tools/ugene, https://sources.debian.org/src/ugene/ | SCR_005579 | 2026-09-03 05:04:05 | 183 | ||||||
|
Yabi Resource Report Resource Website |
Yabi (RRID:SCR_005359) | Yabi | service resource, software resource | A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. | grid computing, high performance computing, cloud computing, bioinformatics, pipeline, workflow, command line, python, linux, storage, compute, genomics, transcriptomics, proteomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Murdoch University; Perth; Australia |
PMID:22333270 | GNU General Public License, v3 | OMICS_01148, biotools:yabi | https://bio.tools/yabi | SCR_005359 | 2026-09-03 05:04:27 | 0 | ||||||
|
HAPLOCLUSTERS Resource Report Resource Website |
HAPLOCLUSTERS (RRID:SCR_007439) | HAPLOCLUSTERS | software application, software resource | Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
Aging | nlx_154014, biotools:haploclusters | https://bio.tools/haploclusters | SCR_007439 | 2026-09-03 05:03:51 | 0 | |||||||
|
PubCrawler Resource Report Resource Website 10+ mentions |
PubCrawler (RRID:SCR_008235) | service resource, software resource | PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. The free PubCrawler web service has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. There is no limit on the number of searches that can be carried out. Previous search hits are stored and only the newest PubMed or GenBank records are shown each day. The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query. This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. Sponsors: Development of PubCrawler was supported by EMBnet | training tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian |
biotools:pubcrawler, nif-0000-21345 | https://bio.tools/pubcrawler | SCR_008235 | PubCrawler | 2026-09-03 05:04:33 | 10 | ||||||||
|
MULTIMAP Resource Report Resource Website 10+ mentions |
MULTIMAP (RRID:SCR_007168) | MULTIMAP | software application, software resource | Software program for automated construction of genetic maps (entry from Genetic Analysis Software) | gene, genetic, genomic, lisp, unix, (sun/compaq-alpha/hp..), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:multimap, nlx_154013 | https://bio.tools/multimap | http://compgen.rutgers.edu/Multimap/ | SCR_007168 | 2026-09-03 05:04:11 | 31 | |||||||
|
SIBMED Resource Report Resource Website 1+ mentions |
SIBMED (RRID:SCR_007495) | SIBMED | software application, software resource | Software application that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 77, ms-windows, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:sibmed, nlx_154043 | https://bio.tools/sibmed | SCR_007495 | SIBling Mutation and Error Detection | 2026-09-03 05:04:24 | 1 | |||||||
|
COEUS Resource Report Resource Website 1+ mentions |
COEUS (RRID:SCR_006287) | COEUS | software application, software resource | A semantic web-powered knowledge management framework, aiming at a streamlined application development cycle and following a semantic web in a box approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. It is targeted at rapid application deployment of new applications in any research field, supported by a comprehensive integration engine and an advanced data distribution API. | data integration, interoperability, ontology, semantic web, bioinformatics, biomedical, semantic web framework, rapid application deployment, linked data, web service, biomedical application, biomedical semantics, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Aveiro; Aveiro; Portugal |
PMID:23244467 | Open unspecified license | biotools:coeus, nlx_151933 | https://bio.tools/coeus | SCR_006287 | 2026-09-03 05:04:20 | 6 | ||||||
|
ASPEX Resource Report Resource Website 1+ mentions |
ASPEX (RRID:SCR_008414) | ASPEX | software application, software resource | A set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, tcl, perl, (the graphic script requires xmgr, available from ftp://ftp.teleport.com/pub/users/pturner/acegr), unix, (solaris/sunos/irix/osf-1), linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154234, biotools:aspex | https://bio.tools/aspex | SCR_008414 | Affected Sib Pairs EXclusion map | 2026-09-03 05:04:14 | 9 | |||||||
|
ASSOCIATIONVIEWER Resource Report Resource Website |
ASSOCIATIONVIEWER (RRID:SCR_009063) | ASSOCIATIONVIEWER | software application, software resource | A Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154050, biotools:association_viewer | https://bio.tools/association_viewer | SCR_009063 | 2026-09-03 05:04:23 | 0 | ||||||||
|
ALBERT Resource Report Resource Website 10+ mentions |
ALBERT (RRID:SCR_009037) | ALBERT | software application, software resource | Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:albert, nlx_154002 | https://bio.tools/albert | SCR_009037 | A Likelihood Based Estimation of Risk in Trios | 2026-09-03 05:04:17 | 48 | |||||||
|
EXOMEPICKS Resource Report Resource Website 1+ mentions |
EXOMEPICKS (RRID:SCR_009174) | EXOMEPICKS | software application, software resource | Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154306, biotools:exomepicks | https://bio.tools/exomepicks | SCR_009174 | 2026-09-03 05:04:03 | 6 | ||||||||
|
DISENTANGLER Resource Report Resource Website 1+ mentions |
DISENTANGLER (RRID:SCR_009161) | DISENTANGLER | software application, software resource | Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, java/jre1.5, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154284, bIotools:disentangler | https://bio.tools/disentangler | SCR_009161 | 2026-09-03 05:04:27 | 6 | ||||||||
|
ALOHOMORA Resource Report Resource Website 1+ mentions |
ALOHOMORA (RRID:SCR_009117) | ALOHOMORA | software application, software resource | Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, ms-window, linux, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154219, biotools:alohomora | https://bio.tools/alohomora | SCR_009117 | 2026-09-03 05:04:21 | 8 | ||||||||
|
CASPAR Resource Report Resource Website 50+ mentions |
CASPAR (RRID:SCR_009074) | CASPAR | software application, software resource | Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:caspar, nlx_154071 | https://bio.tools/caspar | SCR_009074 | Computerized Affected Sibling Pair Analyzer and Reporter | 2026-09-03 05:05:16 | 54 | |||||||
|
genehunter-imprinting Resource Report Resource Website 1+ mentions |
genehunter-imprinting (RRID:SCR_009104) | GENEHUNTER-TWOLOCUS | software application, software resource | Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait. | gene, genetic, genomic, c, unix, sunos, solaris, osf, hpux, aix, ultrix, linux, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
DOI:10.1086/302911 | Resource no longer in service. Documented on February 23,2021 | nlx_154199, biotools:genehunter-imprinting | https://bio.tools/genehunter-imprinting | http://www.staff.uni-marburg.de/~strauchk/software.html | SCR_009104 | GENEHUNTER-MODSCORE, GENEHUNTER-PLUS, GENEHUNTER, GENEHUNTER-IMPRINTING | 2026-09-03 05:04:25 | 1 | ||||
|
CCREL Resource Report Resource Website |
CCREL (RRID:SCR_009142) | CCREL | software application, software resource | Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, perl, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:ccrel, nlx_154261 | https://bio.tools/ccrel | SCR_009142 | Case-Control association analysis with RELlated individuals | 2026-09-03 05:05:18 | 0 |
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