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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nmf Resource Report Resource Website 10+ mentions |
nmf (RRID:SCR_024284) | software toolkit, software resource | Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines. | perform Non-negative Matrix Factorization, nonnegative matrix factorization, | is listed by: Debian | PMID:20598126 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-nmf/ | SCR_024284 | 2026-08-05 10:48:02 | 12 | ||||||||
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proc Resource Report Resource Website 10+ mentions |
proc (RRID:SCR_024286) | software toolkit, software resource | Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves. | visualizing, smoothing and comparing receiver operating characteristic, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_17528 | https://sources.debian.org/src/r-cran-proc/ | SCR_024286 | 2026-08-05 10:48:01 | 32 | ||||||||
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psyphy Resource Report Resource Website |
psyphy (RRID:SCR_024289) | software toolkit, software resource | Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations. | analyzing data from psychophysical experiments, analyzing data, psychophysical experiments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-psyphy/ | SCR_024289 | 2026-08-05 10:48:01 | 0 | |||||||||
|
ruby-bio Resource Report Resource Website |
ruby-bio (RRID:SCR_024322) | software toolkit, software resource | Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. | Ruby programming language, sequence analysis, pathway analysis, protein modelling, phylogenetic analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/ruby-bio/ | SCR_024322 | 2026-08-05 10:48:01 | 0 | |||||||||
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mediana Resource Report Resource Website |
mediana (RRID:SCR_024281) | software toolkit, software resource | Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria. | clinical trial simulations, Clinical Scenario Evaluation approach, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-mediana/ | SCR_024281 | 2026-08-05 10:48:02 | 0 | |||||||||
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itertools Resource Report Resource Website |
itertools (RRID:SCR_024282) | software toolkit, software resource | Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package. | creating iterators, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-itertools/ | SCR_024282 | 2026-08-05 10:48:01 | 0 | |||||||||
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optimalcutpoints Resource Report Resource Website 10+ mentions |
optimalcutpoints (RRID:SCR_024283) | software toolkit, software resource | Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures. | compute optimal cutpoints, selecting optimal cutoffs, analysis and diagnostic test accuracy measures, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-optimalcutpoints/ | SCR_024283 | 2026-08-05 10:48:01 | 10 | |||||||||
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rpact Resource Report Resource Website |
rpact (RRID:SCR_024300) | software toolkit, software resource | Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints. | design and analysis of confirmatory adaptive clinical trials, clinical trials with continuous, binary, survival endpoints, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rpact/ | SCR_024300 | 2026-08-05 10:48:01 | 0 | |||||||||
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shazam Resource Report Resource Website 10+ mentions |
shazam (RRID:SCR_024301) | software toolkit, software resource | Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis. | computational framework, analyzing mutations, immunoglobulin sequences, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29370 | https://sources.debian.org/src/r-cran-shazam/ | SCR_024301 | 2026-08-05 10:48:01 | 27 | ||||||||
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Unicycler Resource Report Resource Website 100+ mentions |
Unicycler (RRID:SCR_024380) | software toolkit, software resource | Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline. | assembly pipeline, bacterial genomes, resolving bacterial genome assemblies, short and long sequencing reads, | is listed by: Debian | PMID:28594827 | Free, Available for download, Freely available, | OMICS_14591 | https://sources.debian.org/src/unicycler/ | SCR_024380 | unicycler | 2026-08-05 10:48:03 | 449 | ||||||
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tab2mage Resource Report Resource Website |
tab2mage (RRID:SCR_024359) | software toolkit, software resource | Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database. | ease process of submitting large microarray experiment datasets, submitting to public repository database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/tab2mage/ | SCR_024359 | Tab2MAGE | 2026-08-05 10:48:02 | 0 | ||||||||
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GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | software application, simulation software, software resource | 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 | 2026-08-05 10:46:49 | 135 | ||||||
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MB-GAN Resource Report Resource Website 1+ mentions |
MB-GAN (RRID:SCR_019289) | software application, simulation software, software resource | 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 | 2026-08-05 10:47:13 | 1 | ||||||
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GNU Octave Resource Report Resource Website 100+ mentions |
GNU Octave (RRID:SCR_014398) | programming language, software resource | A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | command-line, free software, array programming, programming language, mathematics, reproducible research, |
is listed by: Debian is related to: Mastrave modelling library works with: CoSMoMVPA works with: Empirical Gramian Framework |
DOI:10.1016/j.jprocont.2012.04.006 | THIS RESOURCE IS NO LONGER IN SERVICE | https://directory.fsf.org/wiki/Octave, https://sources.debian.org/src/octave/ | SCR_014398 | Octave | 2026-08-05 10:46:09 | 244 | |||||||
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CARD Resource Report Resource Website 100+ mentions |
CARD (RRID:SCR_023995) | data or information resource, database | Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes. | Antibiotic resistance data, resistance genes and associated phenotypes, resistance genes, phenotypes, | is listed by: Debian | PMID:31665441 | Free, Available for download, Freely available | r3d100012727 | https://doi.org/10.17616/R3WN59 | https://sources.debian.org/src/card-rgi/ | SCR_023995 | card-rgi, Comprehensive Antibiotic Resistance Database, The Comprehensive Antibiotic Resistance Database | 2026-08-05 10:47:56 | 211 | |||||
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PILGRM Resource Report Resource Website 1+ mentions |
PILGRM (RRID:SCR_004749) | PILGRIM | data analysis service, production service resource, analysis service resource, service resource | PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis. | data mining, gene expression, user directed data mining, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NIGMS P50 GM071508; NCI T32 CA005928 |
PMID:21653547 | nlx_75372, biotools:pilgrm | https://bio.tools/pilgrm | SCR_004749 | Platform for Interactive Learning by Genomics Results Mining | 2026-08-06 09:26:13 | 1 | |||||
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HSSP Resource Report Resource Website 10+ mentions |
HSSP (RRID:SCR_004953) | HSSP | database, data or information resource | HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. Homologues are very likely to have the same 3D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of sequence aligned sequence families, but it is also a database of implied secondary and tertiary structures. Likely secondary structure are carried over from the PDB protein to each homologous protein. Tertiary structure models can be built by fitting the sequence of the homologue as aligned into the 3D template of the protein of known structure. Special software is needed to construct 3D models by homology, such WHATIF by Gert Vriend or MaxSprout by Liisa Holm and Chris Sander. The command rsync can be used to obtain a local copy of the HSSP. We appreciate receiving an Email from people who do so, but there are no strings attached. Everybody can freely download the files, academia and industry alike. If your institute''s firewall doesn''t allow you to use the (preferred) rsync way of obtaining HSSP files, feel free to work with FTP. The files are in that case available from: ftp://ftp.cmbi.ru.nl//pub/molbio/data/hssp/ | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:2017436 | biotools:hssp, nlx_91976 | https://bio.tools/hssp | SCR_004953 | Homology-derived Secondary Structure of Proteins, homology-derived structures of proteins, HSSP - Homology derived Secondary Structure of Proteins, HSSP database, HSSP - Homology-derived Secondary Structure of Proteins, Homology derived Secondary Structure of Proteins | 2026-08-06 09:26:15 | 33 | ||||||
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STING Report Resource Report Resource Website 1+ mentions |
STING Report (RRID:SCR_005121) | STING | database, data or information resource | Sting Report is a database of amino acid sequences, structures, functions, and parameters. It allows users to easily extract from the Blue Star Sting Database detailed but focused information about an individual amino acid, which belongs to a structure described in a PDB file. The extracted information is presented as a series of GIF images and a table, which are generated by Blue Star Sting modules and contain values of up to 125 sequence/structure/function descriptors/parameters. The HTML page resulting from a query on Sting Report, containing the GIF images and the table, is printable, and can also be composed and visualized at a computer platform with elementary configuration. | amino acid, amino acid function, amino acid sequence, amino acid structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:15608194 | nif-0000-03498, biotools:sting_millenium | https://bio.tools/sting_millenium | SCR_005121 | Blue Star Sting Report | 2026-08-06 09:26:17 | 4 | ||||||
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Information Hyperlinked Over Proteins Resource Report Resource Website 10+ mentions |
Information Hyperlinked Over Proteins (RRID:SCR_004829) | iHOP | service resource, database, data or information resource | Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. | phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Autonomous University of Madrid; Madrid; Spain |
European Union IST-2001- 32688; European Union QLRT-2001-00015 |
PMID:15226743 | Creative Commons Attribution-NoDerivs License, Works v3 | biotools:ihop, nif-0000-00232, OMICS_01185 | https://bio.tools/ihop | SCR_004829 | iHOP - Information Hyperlinked over Proteins | 2026-08-06 09:26:15 | 24 | ||||
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SPOT - Biological prioritization after a SNP association study Resource Report Resource Website 500+ mentions |
SPOT - Biological prioritization after a SNP association study (RRID:SCR_005193) | SPOT | data analysis service, production service resource, analysis service resource, service resource | A web-based tool for using biological databases to prioritize single nucleotide polymorphisms (SNPs) after a genome-wide association study (GWAS). The site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. Users can specify candidate genes or genomic regions with custom levels of prioritization. The results can be downloaded or viewed in the browser where users can interactively explore the details of each SNP, including graphical representations of the genomic information network (GIN) method. For investigators interested in incorporating biological databases into a post-GWAS SNP selection strategy, the SPOT web tool is an easily implemented and flexible solution. | single nucleotide polymorphism, genome-wide association study, linkage disequilibrium, gene, genomic region, p-value, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:20529875 | biotools:spot, OMICS_00189 | https://bio.tools/spot | SCR_005193 | 2026-08-06 09:26:22 | 512 |
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