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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AnnotationHub Resource Report Resource Website 10+ mentions |
AnnotationHub (RRID:SCR_024227) | software resource, software toolkit | Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. | client, Bioconductor AnnotationHub web resource, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29380 | https://sources.debian.org/src/r-bioc-annotationhub/ | SCR_024227 | 2026-08-07 09:30:13 | 28 | ||||||||
|
hypergraph Resource Report Resource Website |
hypergraph (RRID:SCR_024240) | software resource, software toolkit | Software R package that implements some simple capabilities for representing and manipulating hypergraphs. | representing and manipulating hypergraphs, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-hypergraph/ | SCR_024240 | 2026-08-07 09:30:12 | 0 | |||||||||
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htsfilter Resource Report Resource Website 1+ mentions |
htsfilter (RRID:SCR_024242) | software resource, software toolkit | Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions. | filtering procedure, replicated transcriptome sequencing data, global Jaccard similarity index, identify genes with low, constant levels of expression, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-htsfilter/ | SCR_024242 | 2026-08-07 09:30:13 | 6 | |||||||||
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multiassayexperiment Resource Report Resource Website |
multiassayexperiment (RRID:SCR_024245) | software resource, software toolkit | Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis. | harmonize data management, multiple experimental assays, overlapping set of specimens, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_19308 | https://sources.debian.org/src/r-bioc-multiassayexperiment/ | SCR_024245 | 2026-08-07 09:30:13 | 0 | ||||||||
|
mutationalpatterns Resource Report Resource Website 100+ mentions |
mutationalpatterns (RRID:SCR_024247) | software resource, software toolkit | Software R package provides set of flexible functions to evaluate and visualize multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. | evaluate and visualize multitude of mutational patterns, base substitution catalogues patterns, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-mutationalpatterns/ | SCR_024247 | 2026-08-07 09:30:08 | 247 | |||||||||
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groHMM Resource Report Resource Website |
groHMM (RRID:SCR_024237) | software resource, software toolkit | Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data | analysis of GRO-seq data, identifying unannotated and cell type-specific transcription units, global run-on sequencing data, | is listed by: Debian | PMID:26173492 | Free, Available for download, Freely available, | OMICS_07953 | https://sources.debian.org/src/r-bioc-grohmm/ | SCR_024237 | grohmm | 2026-08-07 09:30:12 | 0 | ||||||
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genefilter Resource Report Resource Website 1+ mentions |
genefilter (RRID:SCR_024238) | software resource, software toolkit | Software R package provides some basic functions for filtering genes. | functions for filtering genes | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29382 | https://sources.debian.org/src/r-bioc-genefilter/ | SCR_024238 | 2026-08-07 09:30:07 | 8 | ||||||||
|
seqsero Resource Report Resource Website 10+ mentions |
seqsero (RRID:SCR_024333) | software resource, software toolkit | Software pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. | Salmonella serotype determination, raw sequencing reads, genome assemblies, | is listed by: Debian | PMID:25762776 | Free, Available for download, Freely available, | OMICS_21700 | https://sources.debian.org/src/seqsero/ | SCR_024333 | 2026-08-07 09:30:13 | 17 | |||||||
|
sbmltoolbox Resource Report Resource Website |
sbmltoolbox (RRID:SCR_024329) | software resource, software toolkit | Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave. | functions allowing SBML models to be used in MATLAB and Octave, | is listed by: Debian | PMID:16574696 | Free, Available for download, Freely available, | OMICS_06013 | https://sources.debian.org/src/sbmltoolbox/ | SCR_024329 | 2026-08-07 09:30:15 | 0 | |||||||
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tigger Resource Report Resource Website 1+ mentions |
tigger (RRID:SCR_024310) | software resource, software toolkit | Software R package infers V genotype of individual from immunoglobulin repertoire sequencing data like AIRR-Seq, Rep-Seq. Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among sample sequences. | infer V genotype of individual, immunoglobulin repertoire sequencing data, AIRR-Seq, Rep-Seq, detection of novel alleles, correct existing V allele calls, sample sequences, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_07533 | https://sources.debian.org/src/r-cran-tigger/ | SCR_024310 | 2026-08-07 09:30:09 | 9 | ||||||||
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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 | 2026-08-07 09:30:14 | 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 | 2026-08-07 09:30:13 | 138 | ||||||||
|
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 | 2026-08-07 09:30:10 | 0 | |||||||||
|
rgfa Resource Report Resource Website |
rgfa (RRID:SCR_024323) | software library, software resource, 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 | 2026-08-07 09:30:15 | 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 | 2026-08-07 09:25:02 | 4 | |||||||
|
Unicycler Resource Report Resource Website 500+ 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 | 2026-08-07 09:30:16 | 612 | ||||||
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sourmash Resource Report Resource Website 1+ mentions |
sourmash (RRID:SCR_024347) | software library, software resource, 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 | 2026-08-07 09:30:10 | 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 | 2026-08-07 09:30:10 | 0 | ||||||||
|
CODEHOP Resource Report Resource Website 50+ mentions |
CODEHOP (RRID:SCR_002898) | CODEHOP | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Service to design PCR primers from protein multiple sequence alignments. NOTICE: This version of CODEHOP is no longer maintained. | degenerate, primer, primer design, degenerate primer, oligonucleotide, pcr assay, gene, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Fred Hutchinson Cancer Center |
PMID:20967601 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:codehop, OMICS_02339 | https://bio.tools/codehop | SCR_002898 | COnsensus-DEgenerate Hybrid Oligonucleotide Primers, CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers | 2026-08-07 09:25:32 | 75 | |||||
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DictyOGlyc Resource Report Resource Website 10+ mentions |
DictyOGlyc (RRID:SCR_001600) | DictyOGlyc | analysis service resource, data analysis service, production service resource, 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 | 2026-08-07 09:25:14 | 17 |
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