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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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JAMM Resource Report Resource Website 1+ mentions |
JAMM (RRID:SCR_017049) | data analysis software, software application, software resource, data processing software | Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately. | peak, finder, sequencing, dataset, integrate, replicate, boundary, accurately, bio.tools |
is listed by: Debian is listed by: bio.tools |
Max-Delbrück-Center/New York University Exchange Program. | PMID:25223640 | Free, Available for download, Freely available | biotools:jamm | https://bio.tools/jamm | SCR_017049 | J oint A nalysis of NGS replicates via M ixture M odel clustering, Joint Analysis of NGS replicates via Mixture Model clustering | 2026-08-06 09:29:00 | 2 | |||||
|
REDIportal Resource Report Resource Website 10+ mentions |
REDIportal (RRID:SCR_018490) | atlas, topical portal, service resource, data or information resource, portal, database | Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided. | A-to-I RNA Editing Events, RNA editing events collection, atlas, database, GTEx project, genomic region, gene name, RNAseq, DNAseq, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CLAIRE is related to: SIGNOR |
Italian Ministero dell Istruzione ; Consiglio Nazionale delle Ricerche |
PMID:27587585 | Free, Freely available | biotools:rediportal | https://bio.tools/rediportal | SCR_018490 | 2026-08-06 09:29:26 | 30 | ||||||
|
NetPhos Resource Report Resource Website 100+ mentions |
NetPhos (RRID:SCR_017975) | software resource, standalone software, data access protocol, service resource, production service resource, web service, software application, analysis service resource | Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package. | Neural network, predict, phosphorylation site, independent sequence, protein, kinase, serine, threonine, tyrosine, eukaryotic, bio.tools |
is used by: YinOYang is listed by: Debian is listed by: bio.tools has parent organization: Technical University of Denmark; Lyngby; Denmark |
PMID:10600390 | Free, Freely available | biotools:netphos | https://bio.tools/netphos | http://www.cbs.dtu.dk/services/NetPhos-2.0/ | SCR_017975 | NetPhos 3.1, NetPhos 2.0 | 2026-08-06 09:29:18 | 381 | |||||
|
NanoPipe Resource Report Resource Website 1+ mentions |
NanoPipe (RRID:SCR_016852) | NanoPipe | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms. | analysis, MinION, long, sequence, read, Oxford Nanopore, alignment, target, statistics, polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Muenster; Muenster; Germany |
Institute of Bioinformatics Muenster ; Germany |
PMID:30689855 | Free, Available for download, Freely Available | biotools:NanoPipe | https://github.com/IOB-Muenster/nanopipe2, https://bio.tools/NanoPipe | SCR_016852 | NanoPipe, nanopipe2 | 2026-08-06 09:28:58 | 5 | ||||
|
DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-08-06 09:28:57 | 2 | ||||
|
CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | database, data or information resource | Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site. | carbohydrate, carbohydrate-binding, carbohydrate binding module, carbohydrate esterase, catalytic binding, glycosidic bond, glycosidic hydrolase, glycosyl transferase, polysaccharide lyase, enzyme class, enzyme, module, genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
PMID:24270786 | r3d100012321, biotools:cazy, OMICS_01677, nif-0000-02642, SCR_012935 | https://bio.tools/cazy | SCR_012909 | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-08-06 09:28:01 | 2045 | ||||||
|
ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | web application, software resource | Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction. | web application, prediction, arginine, lysine, cleavage, propeptide, eukaryotic, protein, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/protein/gzh013 | Open source | biotools:prop, BioTools:prop | https://bio.tools/prop, https://bio.tools/prop, https://bio.tools/prop | SCR_014936 | ProP, ProP 1.0 Server, ProP 1.0 | 2026-08-06 09:28:29 | 75 | ||||||
|
Composition Profiler Resource Report Resource Website 10+ mentions |
Composition Profiler (RRID:SCR_014630) | web application, software resource | Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output. | web tool, web application, amino acid, amino acid composition, sequence, bar chart, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17578581 | Source code available, Acknowledgement requested | biotools:composition_profiler | https://bio.tools/composition_profiler | SCR_014630 | 2026-08-06 09:28:25 | 32 | |||||||
|
GeneWise Resource Report Resource Website 1000+ mentions |
GeneWise (RRID:SCR_015054) | web application, software resource | Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool. | gene alignment, dna sequence, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:15123596 | Freely available, Available for download | biotools:wise | https://bio.tools/wise | SCR_015054 | 2026-08-06 09:28:28 | 1017 | |||||||
|
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 | ||||||
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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 | ||||||
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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 | |||||
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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 | ||||||||
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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 | ||||||||
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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 |
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