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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Pscan-ChIP Resource Report Resource Website 1+ mentions |
Pscan-ChIP (RRID:SCR_010885) | Pscan-ChIP | data analysis service, production service resource, analysis service resource, service resource | Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23748563 DOI:10.1093/nar/gkt448 |
biotools:pscanchip, OMICS_00490 | https://bio.tools/pscanchip, https://sources.debian.org/src/pscan-chip/ | SCR_010885 | 2026-08-06 09:27:45 | 5 | |||||||
|
CUPSAT Resource Report Resource Website 50+ mentions |
CUPSAT (RRID:SCR_010773) | CUPSAT | data analysis service, production service resource, analysis service resource, service resource | A tool to predict changes in protein stability upon point mutations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16845001 | biotools:cupsat, OMICS_00128 | https://bio.tools/cupsat | SCR_010773 | Cologne University Protein Stability Analysis Tool, CUPSAT: Cologne University Protein Stability Analysis Tool | 2026-08-06 09:27:44 | 74 | ||||||
|
LS-SNP/PDB Resource Report Resource Website 1+ mentions |
LS-SNP/PDB (RRID:SCR_010774) | LS-SNP/PDB | data analysis service, production service resource, analysis service resource, service resource | A web tool for genome-wide annotation of human SNPs. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_00131, biotools:ls-snp | https://bio.tools/ls-snp | SCR_010774 | 2026-08-06 09:27:40 | 3 | ||||||||
|
Vector Alignment Search Tool Resource Report Resource Website 10+ mentions |
Vector Alignment Search Tool (RRID:SCR_010655) | VAST | production service resource, analysis service resource, service resource | VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages! | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: NCBI Structure has parent organization: NCBI |
PMID:8804824 PMID:8710828 |
nlx_68740, biotools:vast | https://bio.tools/vast | SCR_010655 | Vector Alignment Search Tool (VAST) | 2026-08-06 09:27:42 | 17 | ||||||
|
PlantTFcat Resource Report Resource Website 10+ mentions |
PlantTFcat (RRID:SCR_010898) | PlantTFcat | data analysis service, production service resource, analysis service resource, service resource | A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Samuel Roberts Noble Foundation |
PMID:24219505 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:planttfcat, OMICS_00559 | https://bio.tools/planttfcat | SCR_010898 | PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool | 2026-08-06 09:27:45 | 44 | |||||
|
ArrayPipe Resource Report Resource Website 10+ mentions |
ArrayPipe (RRID:SCR_010934) | ArrayPipe | data analysis service, production service resource, analysis service resource, service resource | A flexible tool for visualizing and analyzing your two-colour microarray slides. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00744, biotools:arraypipe | https://bio.tools/arraypipe | SCR_010934 | 2026-08-06 09:27:41 | 15 | ||||||||
|
PREDDIMER Resource Report Resource Website 10+ mentions |
PREDDIMER (RRID:SCR_011963) | PREDDIMER | data analysis service, production service resource, analysis service resource, service resource | Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24202542 | Free | OMICS_01614, biotools:preddimer | https://bio.tools/preddimer | SCR_011963 | PREDDIMER - Prediction tool for an ensemble of transmembrane ?-helical dimer conformations | 2026-08-06 09:27:50 | 15 | |||||
|
HH-suite Resource Report Resource Website 10+ mentions |
HH-suite (RRID:SCR_016133) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, software application | 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 | 2026-08-06 09:28:46 | 49 | |||||
|
DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software resource, software tool, data analysis software, data processing software, software application | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | 2026-08-06 09:28:42 | 43994 | |||||||
|
Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome. | automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: shovill is hosted by: GitHub |
DOI:10.1371/journal.pone.0112963 DOI:10.1371/journal.pone.0112963 |
Available for download, Acknowledgement requested | OMICS_14553, biotools:pilon | https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ | SCR_014731 | 2026-08-06 09:28:23 | 3102 | |||||||
|
RepeatModeler Resource Report Resource Website 1000+ mentions |
RepeatModeler (RRID:SCR_015027) | sequence analysis software, software resource, data analysis software, data processing software, software application | Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis, sequence repeats, repeat identification, bio.tools |
uses: RepeatScout is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Dfam |
Institute for Systems Biology ; NHGRI R44 HG02244; NHGRI R01 HG002939 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:repeatmodeler | https://bio.tools/repeatmodeler | SCR_015027 | 2026-08-06 09:28:31 | 3193 | |||||||
|
Morpheus Resource Report Resource Website 500+ mentions |
Morpheus (RRID:SCR_014975) | software resource, 3d visualization software, data processing software, data visualization software, software application, simulation software | Modeling and simulation environment for study of multi scale and multicellular systems. Users can construct and simulate models of gene regulation, signaling pathways, tissue patterning and morphogenesis and explore the effects of multiscale feedbacks between these processes. Morpheus can render 2D and 3D models using graphical user interface. | simulation, modeling, multicellular, systems biology, cell-based models, data visualization, differential equations, reaction-diffusion systems, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dresden University of Technology; Saxony; Germany |
BMBF 0315734; BMBF 0316169; DFG |
PMID:24443380 | Free, Available for download, Freely available | biotools:morpheus-framework | https://gitlab.com/morpheus.lab/morpheus, https://bio.tools/morpheus-framework | https://imc.zih.tu-dresden.de/wiki/morpheus | SCR_014975 | 2026-08-06 09:28:31 | 694 | |||||
|
MEBS: Multigenomic Entropy-Based Score Resource Report Resource Website 1+ mentions |
MEBS: Multigenomic Entropy-Based Score (RRID:SCR_015708) | MEBS | data analysis software, software application, software resource, data processing software | Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets. | metagenomics analysis, metabolism, fasta file, protein analysis, omic dataset, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source, Available for download | biotools:mebs | https://bio.tools/mebs | SCR_015708 | metagenome_Pfam_score, Multigenomic Entropy-Based Score, Multigenomic Entropy-Based Score (MEBS) | 2026-08-06 09:28:42 | 1 | ||||||
|
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 | d spatial image, service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | 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 | 2026-08-06 09:28:04 | 0 | |||||
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Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | sequence analysis software, software resource, data analysis software, data processing software, software application | 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 | 2026-08-06 09:29:17 | 602 | ||||||
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | data analysis software, software application, software resource, data processing software | 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 | 2026-08-06 09:29:21 | 13 | |||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | sequence analysis software, software resource, data analysis software, data processing software, software application | 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 | 2026-08-06 09:28:53 | 4072 | ||||||
|
CMap Resource Report Resource Website 100+ mentions |
CMap (RRID:SCR_016204) | data set, software resource, data or information resource, web application, database | 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 | 2026-08-06 09:28:46 | 483 | |||||||
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SMARTdenovo Resource Report Resource Website 100+ mentions |
SMARTdenovo (RRID:SCR_017622) | software resource, image analysis software, alignment software, data processing software, software application | 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 | 2026-08-06 09:29:07 | 159 | ||||||||
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pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | data acquisition software, software resource, image acquisition software, software toolkit, data processing software, software application | 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 | 2026-08-06 09:28:49 | 1068 |
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