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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 resource, software toolkit | 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 | 2026-08-01 12:09:01 | 12 | ||||||||
|
proc Resource Report Resource Website 10+ mentions |
proc (RRID:SCR_024286) | software resource, software toolkit | 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 | 2026-08-01 12:09:01 | 32 | ||||||||
|
psyphy Resource Report Resource Website |
psyphy (RRID:SCR_024289) | software resource, software toolkit | 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 | 2026-08-01 12:08:50 | 0 | |||||||||
|
ruby-bio Resource Report Resource Website |
ruby-bio (RRID:SCR_024322) | software resource, software toolkit | 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 | 2026-08-01 12:08:50 | 0 | |||||||||
|
rgfa Resource Report Resource Website |
rgfa (RRID:SCR_024323) | software resource, software library, software toolkit | Ruby library for handling GFA files. | handling GFA files, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_19578 | https://sources.debian.org/src/ruby-rgfa/ | SCR_024323 | 2026-08-01 12:08:57 | 0 | ||||||||
|
optimalcutpoints Resource Report Resource Website 10+ mentions |
optimalcutpoints (RRID:SCR_024283) | software resource, software toolkit | 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 | 2026-08-01 12:08:56 | 10 | |||||||||
|
rpact Resource Report Resource Website |
rpact (RRID:SCR_024300) | software resource, software toolkit | 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 | 2026-08-01 12:08:56 | 0 | |||||||||
|
shazam Resource Report Resource Website 10+ mentions |
shazam (RRID:SCR_024301) | software resource, software toolkit | 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 | 2026-08-01 12:09:01 | 27 | ||||||||
|
Unicycler Resource Report Resource Website 100+ mentions |
Unicycler (RRID:SCR_024380) | software resource, software toolkit | 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 | 2026-08-01 12:08:57 | 449 | ||||||
|
sourmash Resource Report Resource Website 1+ mentions |
sourmash (RRID:SCR_024347) | software resource, software library, software toolkit | Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets. | MinHash sketching of DNAsearch, | is listed by: Debian | DOI:10.21105/joss.00027 | Free, Available for download, Freely available, | OMICS_21832 | https://sources.debian.org/src/sourmash/ | SCR_024347 | 2026-08-01 12:09:02 | 2 | |||||||
|
tab2mage Resource Report Resource Website |
tab2mage (RRID:SCR_024359) | software resource, software toolkit | 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 | 2026-08-01 12:08:57 | 0 | ||||||||
|
rSeq Resource Report Resource Website 1+ mentions |
rSeq (RRID:SCR_000562) | software resource, software toolkit, source code | 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 | 2026-08-01 12:09:00 | 4 | |||||||
|
DictyOGlyc Resource Report Resource Website 10+ mentions |
DictyOGlyc (RRID:SCR_001600) | DictyOGlyc | data analysis service, service resource, production service resource, analysis 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 | 2026-08-01 12:08:59 | 14 | |||||
|
GlyProt Resource Report Resource Website 10+ mentions |
GlyProt (RRID:SCR_001560) | GlyProt | data analysis service, service resource, production service resource, analysis 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 | 2026-08-01 12:08:59 | 39 | |||
|
Phospho.ELM Resource Report Resource Website 10+ mentions |
Phospho.ELM (RRID:SCR_001109) | data or information resource, database | 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 | 2026-08-01 12:09:03 | 40 | |||||||
|
HiPipe Resource Report Resource Website 1+ mentions |
HiPipe (RRID:SCR_001215) | HiPipe | data analysis service, service resource, production service resource, analysis 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 | 2026-08-01 12:09:08 | 2 | ||||||
|
ImJoy Resource Report Resource Website 1+ mentions |
ImJoy (RRID:SCR_020935) | data processing software, data analysis software, software application, software resource | Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers. | Deep learning, flexible plugin system, deploying deep learning applications, advanced image analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download,Freely available | biotools:ImJoy | https://github.com/imjoy-team/ImJoy, https://bio.tools/ImJoy | SCR_020935 | 2026-08-01 12:07:01 | 3 | ||||||||
|
UEA sRNA Workbench Resource Report Resource Website 1+ mentions |
UEA sRNA Workbench (RRID:SCR_020947) | data processing software, data analysis software, software application, software resource | Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals. | Analysing small RNA data, analyzing miRNAs, profiling small RNA expression patterns, genetic data, bio.tools, bio.tools, bio.tools |
lists: VisSR is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
BBSRC BB/L021269/1 | PMID:29722807 | Free, Available for download, Freely available | biotools:siloco, biotools:mircat | https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench, https://bio.tools/mircat, https://bio.tools/siloco, | SCR_020947 | UEA small RNA Workbench | 2026-08-01 12:07:10 | 7 | |||||
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covtobed Resource Report Resource Website |
covtobed (RRID:SCR_023998) | softwre application | Software tool to generate BED coverage tracks from BAM files. | generate BED coverage tracks, BAM files, | is listed by: Debian | DOI:10.21105/joss.02119 | Free, Available for download, Freely available | https://sources.debian.org/src/covtobed/ | SCR_023998 | 2026-08-01 12:08:24 | 0 | ||||||||
|
GramAlign Resource Report Resource Website 1+ mentions |
GramAlign (RRID:SCR_024032) | image analysis software, alignment software, software application, software resource, data processing software | Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences. | Multiple Sequence Alignment, progressive Multiple Sequence Alignment, sequence distance estimation, nucleotide and amino acid sequences, | is listed by: Debian | Free, Freely available | OMICS_05314 | https://sources.debian.org/src/gramalign/ | SCR_024032 | gramalign | 2026-08-01 12:07:59 | 4 |
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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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