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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RNA FRABASE - RNA FRAgments search engine and dataBASE Resource Report Resource Website |
RNA FRABASE - RNA FRAgments search engine and dataBASE (RRID:SCR_012808) | RNA FRABASE | data analysis service, data or information resource, database, service resource, d spatial image, production service resource, analysis service resource | Engine and database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation. The database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types given for the PBD-deposited RNA structures. Knowledge of the three dimensional RNA structure is crucial for all fields of biomolecular research. In contrast to the protein field, only about 1.300 experimentally derived structures of RNAs are deposited in the Protein Data Bank (PDB). To complement the results of experimental studies, new approaches based on bioinformatics and calculation are pursued in several laboratories to make tertiary RNA structure prediction possible. RNA FRABASE version 2.0 should greatly facilitate various RNA structure modelling approaches, RNA structure analysis and motif searching. If one compares the three dimensional RNA structure to a spatial puzzle, the RNA FRABASE allows to pull out a defined piece of this puzzle - the 3D RNA fragment. The architecture of the web-accessible RNA FRABASE engine and database is based on the following information path: PDB-deposited RNA structures �� RNA sequences and secondary structures described in the dot-bracket notation �� secondary structures of RNA fragments �� 3D RNA fragments. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide on the spot structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. | structural element, secondary structure, rna, rna structure, 3d rna fragment, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Polish Academy of Sciences Poznan; Poznan; Poland |
Foundation for Polish Science SP 01/04; Ministry of Education and Science 3T09A014 29; Polish Ministry of Science and Higher Education PBZ-MniSW-07/1/2007/01; Polish Ministry of Science and Higher Education NN 519314635 |
PMID:20459631 PMID:17921499 |
nif-0000-03413, biotools:rna_frabase | https://bio.tools/rna_frabase | SCR_012808 | RNA FRAgments search engine dataBASE, RNA FRAgments search engine and dataBASE, RNA FRABASE - RNA FRAgments search engine dataBASE | 2026-07-31 09:27:09 | 0 | |||||
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GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | software resource, software application, simulation software | Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species. | Homology, based, gene, prediction, model, target, evolutionary, related, reference, species, sequence, conservation, intron, position, RNAseq, data, protein, coding, transcript, bio.tools |
is listed by: bio.tools is listed by: Debian works with: GUSHR |
PMID:31020559 | Free, Available for download, Freely available | biotools:gemoma | https://bio.tools/gemoma | SCR_017646 | Gene Model Mapper | 2026-07-31 09:28:11 | 135 | ||||||
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Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | 2026-07-31 09:28:13 | 602 | ||||||
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | data processing software, data analysis software, software application, software resource | Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. | High density genotyping data, molecular phenotype, gene expression, proteomics, mapping trait loci, diversity outbred mice, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM074244; NIGMS R01 GM070683; NIGMS R01 GM123489 |
PMID:30591514 | Free, Available for download, Freely available | biotools:R_qtl2, SCR_020965 | https://bio.tools/R_qtl2, https://kbroman.org/qtl2, https://github.com/rqtl/qtl2 | SCR_018181 | QTL, R/quantitative trait loci, QTL2, Quantitative Trait Locus 2, quantitative trait loci 2, R/qtl, qtl2 | 2026-07-31 09:28:27 | 13 | |||||
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Berkeley Advanced Reconstruction Toolbox Resource Report Resource Website 1+ mentions |
Berkeley Advanced Reconstruction Toolbox (RRID:SCR_016168) | BART | image analysis software, image reconstruction software, software application, software resource, data processing software | Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. | mri, reconstruction, magnetic, resonance, neuroimaging, array, transform, algorithm | is listed by: Debian | NCRR R41 RR09784; American Heart Association 12BGIA9660006; NIBIB R01 EB009690; UC Discovery 193037; Sloan Research Fellowship ; GE Healthcare |
Open source, Free | https://mrirecon.github.io/bart/, https://sources.debian.org/src/bart/ | SCR_016168 | 2026-07-31 09:27:52 | 7 | |||||||
|
StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-07-31 09:27:57 | 4072 | ||||||
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CMap Resource Report Resource Website 100+ mentions |
CMap (RRID:SCR_016204) | data or information resource, database, web application, data set, software resource | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-07-31 09:27:53 | 483 | |||||||
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Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution. | long, read, genome, assembly, hinging, sequence, optimal, repeat, resolution |
is listed by: Debian is listed by: OMICtools |
PMID:28320918 | Free, Available for download | OMICS_12339 | https://sources.debian.org/src/hinge/ | SCR_016135 | 2026-07-31 09:27:55 | 9 | |||||||
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HH-suite Resource Report Resource Website 10+ mentions |
HH-suite (RRID:SCR_016133) | software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments. | protein, sensitive sequence search, pairwise alignment, multiple database, homologous structure, prediction, modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
the Deutsche Forschungsgemeinschaft grant SFB646; Ludwig-Maximilians Universität Munich ; Excellence Initiative of the Bundesministerium für Bildung und Forschung |
DOI:10.1186/s12859-019-3019-7 | Free, Available for download, Freely available | biotools:hh-suite | https://bio.tools/hh-suite | http://toolkit.genzentrum.lmu.de/sections/search | SCR_016133 | 2026-07-31 09:27:56 | 49 | |||||
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SMARTdenovo Resource Report Resource Website 100+ mentions |
SMARTdenovo (RRID:SCR_017622) | image analysis software, alignment software, software application, software resource, data processing software | Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus. | De novo, assembler, PacBio, Oxford Nanopore, data, sequence, raw, read, alignment, error, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:SMARTdenovo, biotools:SMARtdenovo | https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo | SCR_017622 | 2026-07-31 09:28:22 | 159 | ||||||||
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pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | software toolkit, data acquisition software, software application, software resource, data processing software, image acquisition software | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap, https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf, https://bio.tools/pheatmap, https://sources.debian.org/src/r-cran-pheatmap/ | SCR_016418 | pretty heatmap | 2026-07-31 09:27:57 | 1068 | ||||||
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FreeContact Resource Report Resource Website 10+ mentions |
FreeContact (RRID:SCR_016113) | image analysis software, alignment software, software application, software resource, data processing software | Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud). | protein, structure, prediction, sequence, analysis, fast, contact, alignment, multiple |
is listed by: OMICtools is related to: Debian |
Alexander von Humboldt Foundation ; German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung) ; Research Council of Norway 208481 |
PMID:24669753 DOI:10.1186/1471-2105-15-85 |
Open source, Free, Available for download | OMICS_03520 | https://rostlab.org/owiki/index.php/FreeContact, https://sources.debian.org/src/libfreecontact-perl/ | SCR_016113 | 2026-07-31 09:27:56 | 21 | ||||||
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JAMM Resource Report Resource Website 1+ mentions |
JAMM (RRID:SCR_017049) | data processing software, data analysis software, software application, software resource | 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 | 2026-07-31 09:28:04 | 2 | |||||
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NetPhos Resource Report Resource Website 100+ mentions |
NetPhos (RRID:SCR_017975) | data access protocol, service resource, software application, production service resource, software resource, standalone software, web service, 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 | 2026-07-31 09:28:23 | 381 | |||||
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NanoPipe Resource Report Resource Website 1+ mentions |
NanoPipe (RRID:SCR_016852) | NanoPipe | data analysis service, data access protocol, service resource, production service resource, software resource, analysis service resource, web service | 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 | 2026-07-31 09:28:04 | 5 | ||||
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, software application, software resource, sequence analysis software, data processing software | 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 | 2026-07-31 09:28:08 | 2 | ||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT082930MA; National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882 |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-07-31 09:27:55 | 8 | ||||||
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REDIportal Resource Report Resource Website 10+ mentions |
REDIportal (RRID:SCR_018490) | data or information resource, portal, database, service resource, topical portal, atlas | 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 | 2026-07-31 09:28:16 | 30 | ||||||
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MB-GAN Resource Report Resource Website 1+ mentions |
MB-GAN (RRID:SCR_019289) | software resource, software application, simulation software | Software tool as deep learning simulation framework for simulating realistic microbiome data. Can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from it. | Metagenomics, deep learning, generative adversarial network, microbiome data simulation, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Texas at Dallas; Texas; USA |
DOI:10.1101/863977 | Free, Available for download, Freely available | biotools:mb-gan | https://bio.tools/mb-gan | SCR_019289 | Microbiome Simulation via Generative Adversarial Network | 2026-07-31 09:28:49 | 1 | ||||||
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SOAPnuke Resource Report Resource Website 1000+ mentions |
SOAPnuke (RRID:SCR_015025) | data analysis software, software application, software resource, sequence analysis software, data processing software | Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status. | sequence data, fastq, dge dataset, rna, metagenomics, bio.tools |
is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Open Source, Free | biotools:soapnuke | https://bio.tools/soapnuke | SCR_015025 | 2026-07-31 09:27:43 | 1447 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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