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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, image analysis software, software application, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-09-19 12:56:05 | 15 | ||||||
|
PASTEClassifier Resource Report Resource Website 10+ mentions |
PASTEClassifier (RRID:SCR_017645) | PASTEC | data processing software, software application, software resource | Software tool for automatic transposable element classification. Used for searching for structural features and similarity to classify transposable elements. | Automatic, transposable, element, classification, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
French National Research Agency | PMID:24786468 | Free, Available for download, Freely available | biotools:PAStEClassifier | https://urgi.versailles.inra.fr/download/repet/PASTEClassifier-1.0.tar.gz, https://bio.tools/repet, https://bio.tools/PASTEClassifier | SCR_017645 | Pseudo Agent System for Transposable Elements Classification, PASTEC | 2026-09-19 12:56:08 | 12 | ||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | data processing software, software application, software resource | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-09-19 12:56:08 | 76 | ||||||
|
MEGAHIT Resource Report Resource Website 1000+ mentions |
MEGAHIT (RRID:SCR_018551) | data processing software, software application, software resource | Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server. | NGS metagenome, Next Generation Sequencing assembler, metagenome, genome assembly, genome sequence, metagenomic dataset, giga base pairs, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Hong Kong GRF ; Innovation and Technology Fund |
PMID:25609793 PMID:27012178 |
Free, Available for download, Freely available | OMICS_07234, biotools:megahit | https://bio.tools/megahit, https://sources.debian.org/src/megahit/ | SCR_018551 | MEGAHIT v0.1 | 2026-09-19 12:56:10 | 1897 | |||||
|
TGS-GapCloser Resource Report Resource Website 10+ mentions |
TGS-GapCloser (RRID:SCR_017633) | data processing software, software application, software resource | Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes. | Error, prone, third, generation, sequencing, long, read, gap, closing, genome, assembly, contig, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:tGS-GapCloser | https://bio.tools/TGS-GapCloser | SCR_017633 | 2026-09-19 12:56:08 | 45 | ||||||||
|
mosdepth Resource Report Resource Website 50+ mentions |
mosdepth (RRID:SCR_018929) | data processing software, software application, software resource | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NCI U24 CA209999; NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-09-19 12:56:10 | 56 | ||||||
|
parSMURF Resource Report Resource Website 1+ mentions |
parSMURF (RRID:SCR_017560) | data processing software, software application, software resource | Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants. | High, performance, computing, imbalance, aware, machine, learning, genome, wide, detection, pathogenic, variant, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parsmurf | https://bio.tools/parsmurf | SCR_017560 | 2026-09-19 12:56:08 | 1 | ||||||||
|
EHRtemporalVariability Resource Report Resource Website 1+ mentions |
EHRtemporalVariability (RRID:SCR_018663) | data processing software, software application, software resource | Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users. | Delineating temporal data set shift, data set shift, electronic health record, temporal variability, delineate temporal data set shift, data dissimilarities, reliable data reuse, examine data set, biomedical data reuse, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Shiny |
DOI:10.1101/2020.04.07.20056564 | Free, Available for download, Freely available | biotools:ehrtemporalvariability | https://cran.r-project.org/web/packages/EHRtemporalVariability/readme/README.html, https://bio.tools/ehrtemporalvariability | SCR_018663 | Electronic Health Records temporal variability | 2026-09-19 12:56:10 | 3 | ||||||
|
PyBEL Resource Report Resource Website 1+ mentions |
PyBEL (RRID:SCR_017660) | software resource, software toolkit | Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. | Parsing, validating, compiling, converting, network, BEL, biological, expression, language, bio.tools |
is used by: Bio2BEL is listed by: bio.tools is listed by: Debian is related to: Biological Expression Language |
European Union/European Federation of Pharmaceutical Industries and Associations (EFPIA) Innovative Medicines Initiative Joint Undertaking | PMID:29048466 | Free, Available for download, Freely available | biotools:pybel, SCR_024180 | https://github.com/pybel/pybel, https://bio.tools/pybel/, https://pybel.readthedocs.io | https://sources.debian.org/src/python3-pybel/ | SCR_017660 | pybel, Python Biological Expression Language | 2026-09-19 12:56:08 | 1 | ||||
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rna-stability Resource Report Resource Website 1+ mentions |
rna-stability (RRID:SCR_019259) | data processing software, software application, software resource | Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species. | Secondary RNA structures generation, large scale generation, RNA structures, transcriptome folding statistics, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:rna-stability | https://bio.tools/rna-stability | SCR_019259 | 2026-09-19 12:56:11 | 1 | ||||||||
|
RADAR-base Resource Report Resource Website 1+ mentions |
RADAR-base (RRID:SCR_019233) | data or information resource, portal, project portal | Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way. | Data collection, remote data collection, data collection platform, collecting mHealth datasets, mental health, mobile applications, remote sensing technology, telemedicine, bio.tools |
is listed by: bio.tools is listed by: Debian |
EU IMI2 ; GSTT Charity ; King’s College London ; Maudsley Charity ; Maudsley NHS Foundation Trust ; NIHR Biomedical Research Centre at South London ; UK National Institute for Health Research |
Free, Available for download, Freely available | biotools:RADAR-base | https://radar-base.org/index.php/getting-started-with-radar-base/, https://radar-base.org/index.php/getting-started-with-radar-base/demo-using-prmt-app/, https://bio.tools/RADAR-base | SCR_019233 | Remote Assessment of Disease And Relapses, Radar-base | 2026-09-19 12:56:11 | 1 | ||||||
|
SeqEM Resource Report Resource Website 1+ mentions |
SeqEM (RRID:SCR_002021) | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Online tool for utilizing a genotype calling algorithm for next-generation sequence data. | genotype, algorithm, sequence, rna, dna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Miami Miller School of Medicine; Florida; USA |
PMID:20861027 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00074, biotools:seqem | https://bio.tools/seqem | SCR_002021 | 2026-09-19 12:55:04 | 1 | |||||||
|
BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase, https://doi.org/10.17616/R3G61K | http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | 2026-09-19 12:55:04 | 82 | ||||
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SGA Resource Report Resource Website 10+ mentions |
SGA (RRID:SCR_001982) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package that functions as a de novo genome assembler based on the concept of string graphs. It is designed as a modular set of programs used to assemble large genomes from high coverage short read data. | string, graph assembler, de novo assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
DOI:10.1101/gr.126953.111 | Free, Available for download, Freely available | OMICS_00028, biotools:sga | https://bio.tools/sga, https://sources.debian.org/src/sga/ | SCR_001982 | String Graph Assembler (SGA), String Graph Assembler | 2026-09-19 12:55:04 | 18 | ||||||
|
GSNAP Resource Report Resource Website 500+ mentions |
GSNAP (RRID:SCR_005483) | GSNAP | alignment software, data processing software, image analysis software, software application, software resource | Software to align single and paired end reads as short as 14 nt and of arbitrarily long length. Can detect short and long distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or database of known splice sites. Permits SNP-tolerant alignment to reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for study of methylation state. | next-generation sequencing, bio.tools, FASEB list |
is used by: Gsnap2Augustus is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20147302 | OMICS_00665, biotools:gsnap | https://bio.tools/gsnap | SCR_005483 | Genomic Short-read Nucleotide Alignment Program | 2026-09-19 12:55:08 | 802 | ||||||
|
EMAGE Gene Expression Database Resource Report Resource Website 10+ mentions |
EMAGE Gene Expression Database (RRID:SCR_005391) | EMAGE | atlas, data or information resource, data repository, database, service resource, storage service resource | A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without. | genetics, 3d model, anatomy, development, mouse morphology, molecular neuroanatomy resource, gene expression, in situ hybridization, immunohistochemistry, embryo, in situ reporter, embryonic mouse, optical projection tomography, confocal microscopy, annotation, pathway, gene association, protein, theiler stage, gene expression, embryology, dna, protein, protein-protein interaction, protein binding, gene, embryology, anatomy, genetics, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: HUDSEN Electronic Atlas of the Developing Human Brain is related to: eMouseAtlas is related to: eMouseAtlas is related to: HUDSEN Human Gene Expression Spatial Database is related to: aGEM is related to: Eurexpress is related to: Gene Expression Database is related to: Gene Ontology is related to: NIDDK Information Network (dkNET) is related to: GUDMAP Ontology |
MRC | PMID:19767607 | Except where noted, Creative Commons Attribution License, The community can contribute to this resource | biotools:emage, nif-0000-00080, r3d100010564 | https://bio.tools/emage, https://doi.org/10.17616/R3860B | SCR_005391 | Emage (e-Mouse Atlas of Gene Expression), e-Mouse Atlas of Gene Expression | 2026-09-19 12:55:08 | 25 | ||||
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ATRHUNTER Resource Report Resource Website 1+ mentions |
ATRHUNTER (RRID:SCR_006480) | ATRHUNTER | analysis service resource, data analysis service, production service resource, service resource, software resource | Software that finds and displays approximate tandem repeats in DNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16201913 | biotools:atrhunter, OMICS_00102 | https://bio.tools/atrhunter | SCR_006480 | 2026-09-19 12:55:09 | 1 | |||||||
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LAST Resource Report Resource Website 100+ mentions |
LAST (RRID:SCR_006119) | LAST | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence alignment, align, vertebrate, genome, sequence, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: RecountDB has parent organization: National Institute of Advanced Industrial Science and Technology |
National Genome Research Network ; INTEuropean Union Systems Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:21209072 PMID:20144198 PMID:20110255 DOI:10.1093/nar/gkq010 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151594, OMICS_15813, biotools:last | https://bio.tools/last, https://sources.debian.org/src/last-align/ | SCR_006119 | 2026-09-19 12:55:08 | 403 | |||||
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GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-09-19 12:55:09 | 353 | ||||
|
ClinVar Resource Report Resource Website 5000+ mentions |
ClinVar (RRID:SCR_006169) | ClinVar | data or information resource, data repository, database, service resource, storage service resource | 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 | 2026-09-19 12:55:09 | 7407 |
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