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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PyCogent Resource Report Resource Website 1+ mentions |
PyCogent (RRID:SCR_024192) | software resource, software library, software toolkit | Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. | analysis of genomic sequence data, generating publication quality graphics, | is listed by: Debian | PMID:17708774 | Free, Available for download, Freely available, | OMICS_14006 | https://sources.debian.org/src/python3-cogent3/ | SCR_024192 | python-cogent, COmparative GENomic Toolkit | 2026-08-01 12:08:59 | 2 | ||||||
|
Cooler Resource Report Resource Website 100+ mentions |
Cooler (RRID:SCR_024194) | software resource, software library, software toolkit | Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays. | store genomic interaction data, scalable storage for Hi-C data, genomically labeled arrays storage, | is listed by: Debian | PMID:31290943 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-cooler/ | SCR_024194 | python-cooler | 2026-08-01 12:08:47 | 159 | |||||||
|
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 | 2026-08-01 12:08:59 | 24 | ||||||||
|
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 | 2026-08-01 12:09:00 | 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 | 2026-08-01 12:09:00 | 5 | |||||||||
|
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 | 2026-08-01 12:08:55 | 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 | 2026-08-01 12:08:48 | 220 | |||||||||
|
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 | 2026-08-01 12:08:59 | 0 | ||||||
|
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 | 2026-08-01 12:08:55 | 7 | ||||||||
|
rann Resource Report Resource Website 1+ mentions |
rann (RRID:SCR_024297) | software resource, software toolkit | Software R package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). | k nearest neighbours finding, every point in given dataset in O(N log N) time, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rann/ | SCR_024297 | 2026-08-01 12:08:56 | 5 | |||||||||
|
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 | 2026-08-01 12:08:57 | 15 | |||||||
|
rnexml Resource Report Resource Website |
rnexml (RRID:SCR_024291) | software resource, software toolkit | Software R package provides access to phyloinformatic data in 'NeXML' format. | access to phyloinformatic data in 'NeXML' format, phyloinformatic data, NeXML format, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rnexml/ | SCR_024291 | 2026-08-01 12:09:01 | 0 | |||||||||
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phylobase Resource Report Resource Website 1+ mentions |
phylobase (RRID:SCR_024292) | software resource, software toolkit | Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis. | associate, manipulate, explore, plot, phylogenetic trees and data, phylogenetic analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-phylobase/ | SCR_024292 | 2026-08-01 12:08:50 | 1 | |||||||||
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qqman Resource Report Resource Website 10+ mentions |
qqman (RRID:SCR_024293) | software resource, software toolkit | Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files. | create Q-Q and manhattan plots, GWAS data, PLINK output files, | is listed by: Debian | DOI:10.1101/005165 | Free, Available for download, Freely available, | OMICS_12451 | https://sources.debian.org/src/r-cran-qqman/ | SCR_024293 | 2026-08-01 12:08:56 | 12 | |||||||
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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 | 2026-08-01 12:09:02 | 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 | 2026-08-01 12:09:01 | 8 | ||||||||
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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 | ||||||||
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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 | |||||||||
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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 |
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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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