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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Open Babel Resource Report Resource Website 50+ mentions |
Open Babel (RRID:SCR_014920) | software application, data analytics software, data processing software, software resource | Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats. | toolbox, conversion, analysis, molecular model, chemistry, biochemistry, chemical file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:open_babel | https://bio.tools/open_babel | SCR_014920 | 2026-08-06 09:28:26 | 81 | ||||||||
|
GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | portal, dataset, project portal, data or information resource | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-08-06 09:28:31 | 7700 | |||||
|
xia2 pipeline Resource Report Resource Website 10+ mentions |
xia2 pipeline (RRID:SCR_015746) | software application, data processing software, software resource | Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities. | xray, diffraction, data processing, synchrotron, mmulti-pass, multi-wavelength, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23793152 | Open Source, Available for download | biotools:xia2 | https://bio.tools/xia2 | SCR_015746 | 2026-08-06 09:28:43 | 34 | |||||||
|
rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | software application, data processing software, software resource | Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software. | evaluation, quality, RNA-Seq, assembly, data, transcriptome, assembler, reference, genome, gene, database, raw, read, , bio.tools |
uses: BUSCO is listed by: Debian is listed by: bio.tools is related to: rnaSPAdes is related to: Python Programming Language is related to: SPAdes |
EMC Research and Development Department ; St. Petersburg State University ; Russia |
PMID:27153654 | Free, Available for download, Freely available | biotools:rnaQUASt | https://bio.tools/rnaQUAST | SCR_016994 | 2026-08-06 09:28:59 | 3 | ||||||
|
Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | image analysis software, software application, data processing software, 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 | 2026-08-06 09:28:49 | 13 | ||||||
|
PASTEClassifier Resource Report Resource Website 10+ mentions |
PASTEClassifier (RRID:SCR_017645) | PASTEC | software application, data processing software, 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 | 2026-08-06 09:29:10 | 11 | ||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, data processing software, 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 | 2026-08-06 09:29:07 | 59 | ||||||
|
MEGAHIT Resource Report Resource Website 1000+ mentions |
MEGAHIT (RRID:SCR_018551) | software application, data processing software, 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 | 2026-08-06 09:29:27 | 1451 | |||||
|
TGS-GapCloser Resource Report Resource Website 10+ mentions |
TGS-GapCloser (RRID:SCR_017633) | software application, data processing software, 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 | 2026-08-06 09:29:10 | 35 | ||||||||
|
parSMURF Resource Report Resource Website 1+ mentions |
parSMURF (RRID:SCR_017560) | software application, data processing software, 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 | 2026-08-06 09:29:06 | 1 | ||||||||
|
EHRtemporalVariability Resource Report Resource Website 1+ mentions |
EHRtemporalVariability (RRID:SCR_018663) | software application, data processing software, 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 | 2026-08-06 09:29:28 | 3 | ||||||
|
rna-stability Resource Report Resource Website 1+ mentions |
rna-stability (RRID:SCR_019259) | software application, data processing software, 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 | 2026-08-06 09:29:27 | 1 | ||||||||
|
mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | software application, data processing software, 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 |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-08-06 09:29:24 | 38 | ||||||
|
RADAR-base Resource Report Resource Website 1+ mentions |
RADAR-base (RRID:SCR_019233) | portal, project portal, data or information resource | 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 |
GSTT Charity ; Maudsley Charity ; NIHR Biomedical Research Centre at South London ; Maudsley NHS Foundation Trust ; King’s College London ; EU IMI2 ; 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 | 2026-08-06 09:29:32 | 1 | ||||||
|
rSeq Resource Report Resource Website 1+ mentions |
rSeq (RRID:SCR_000562) | source code, software toolkit, software resource | A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations. | rna, sequence, read quality assessment, reference sequence generation, sequence mapping, gene, isoform expressions estimations, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
Free, Available for download, Freely available, | OMICS_01288, biotools:rseq | https://bio.tools/rseq | SCR_000562 | RNA-Seq Analyzer, rSeq: RNA-Seq Analyzer | 2026-08-06 09:25:13 | 4 | |||||||
|
DictyOGlyc Resource Report Resource Website 10+ mentions |
DictyOGlyc (RRID:SCR_001600) | DictyOGlyc | data analysis service, production service resource, analysis service resource, service resource | Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins. | glcnac glycosylation site, neural network, o-glycosylation, prediction, proteome, glycoprotein, glcnac, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Deutscher Akademischer Austauschdienst ; HspII/AUFE ; Macquarie University International Postgraduate Research Award ; Australian Research Council ; National Health and MRC ; Danish National Research Foundation |
PMID:10521537 | Free, Freely available | nlx_153856, biotools:dictyoglyc | https://bio.tools/dictyoglyc | SCR_001600 | 2026-08-06 09:25:26 | 14 | |||||
|
GlyProt Resource Report Resource Website 10+ mentions |
GlyProt (RRID:SCR_001560) | GlyProt | data analysis service, production service resource, analysis service resource, service resource | Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php | glycosylation, protein, in silico, 3d structure, protein structure, glycan, n-glycan, glycoprotein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: SWEET-DB has parent organization: glycosciences.de |
DFG | PMID:15980456 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:glyprot, nlx_152875 | https://bio.tools/glyprot | http://www.glycosciences.de/glyprot/ | SCR_001560 | GlyProt - In Silico Glycosylation of Proteins | 2026-08-06 09:25:24 | 39 | |||
|
Phospho.ELM Resource Report Resource Website 10+ mentions |
Phospho.ELM (RRID:SCR_001109) | database, data or information resource | Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database. | eukaryotic protein, phosphorylation site, database, curation, bio.tools, FASEB list |
uses: UniProt is listed by: bio.tools is listed by: Debian has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:17962309 | Publicly available | nif-0000-03278, biotools:phosphoelm | https://bio.tools/phosphoelm | SCR_001109 | 2026-08-06 09:25:20 | 40 | |||||||
|
HiPipe Resource Report Resource Website 1+ mentions |
HiPipe (RRID:SCR_001215) | HiPipe | data analysis service, production service resource, analysis service resource, service resource | Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task. | next-generation sequencing, dna, rna, differential expression, mirna, gene fusion, variant, genome, exome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Academia Sinica; Taipei; Taiwan |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02128, biotools:hipipe | https://bio.tools/hipipe | SCR_001215 | HiPipe - High Performance Pipelines for NGS Data Analysis | 2026-08-06 09:25:21 | 2 | ||||||
|
A Classification of Mobile genetic Elements Resource Report Resource Website 10+ mentions |
A Classification of Mobile genetic Elements (RRID:SCR_001694) | ACLAME | database, data or information resource | A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME. | mobile genetic element, phage genome, plasmid, virus, prophage, transposon, protein, gene, classification, data analysis service, prophage prediction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Free University of Brussels; Brussels; Belgium is parent organization of: MeGO |
ESTEC contract ESTEC 16370/02/NL/CK | PMID:19933762 PMID:14681355 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02533, OMICS_01528, biotools:aclame | https://bio.tools/aclame | SCR_001694 | ACLAME: A CLAssification of Mobile genetic Elements | 2026-08-06 09:25:27 | 31 |
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