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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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wavethresh Resource Report Resource Website 1+ mentions |
wavethresh (RRID:SCR_024311) | software resource, software toolkit | Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation. | perform 1D, 2D and 3D real and complex valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage, data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-wavethresh/ | SCR_024311 | 2026-08-01 12:08:57 | 3 | |||||||||
|
webgestaltr Resource Report Resource Website 100+ mentions |
webgestaltr (RRID:SCR_024312) | software resource, software toolkit | Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results. | gene set enrichment analysis, network topology analysis, simultaneously analyze multiple gene lists, exploration of enrichment results, |
is listed by: Debian is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit |
Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-webgestaltr/ | SCR_024312 | WebGestaltR | 2026-08-01 12:09:02 | 125 | ||||||||
|
sjplot Resource Report Resource Website 100+ mentions |
sjplot (RRID:SCR_024307) | software resource, software toolkit | Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data. | data visualization, simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-sjplot/ | SCR_024307 | 2026-08-01 12:08:56 | 105 | |||||||||
|
waveslim Resource Report Resource Website |
waveslim (RRID:SCR_024308) | software resource, software toolkit | Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis. | wavelet routines, time series, 1D analysis, image 2D analysis, array 3D analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-waveslim/ | SCR_024308 | 2026-08-01 12:09:01 | 0 | |||||||||
|
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 | ||||||||
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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 | |||||
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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 | |||
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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 | |||||||
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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 |
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