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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Orthology.eg.db Resource Report Resource Website 1+ mentions |
Orthology.eg.db (RRID:SCR_024740) | software toolkit, software resource | Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings. | orthology mappings between species, NCBI Gene IDs, NCBI orthology mappings, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024740 | 2026-02-15 09:23:36 | 1 | ||||||||||
|
ExperimentHub Resource Report Resource Website 1+ mentions |
ExperimentHub (RRID:SCR_024820) | software toolkit, software resource | Software R package provides central location where curated data from experiments, publications or training courses can be accessed. | data access, curated data from experiments, publications data, training courses data, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024820 | 2026-02-15 09:23:38 | 2 | ||||||||||
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | software application, data processing software, software toolkit, data analysis software, software resource | Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. | copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:21486749 | Free, Available for download, Freely available | biotools:cn.farms, OMICS_02060 | https://bio.tools/cn.farms | SCR_000289 | cn.farms - factor analysis for copy number estimation | 2026-02-16 09:45:13 | 0 | |||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | software application, data processing software, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | CorMut - Detect the correlated mutations based on selection pressure | 2026-02-16 09:45:10 | 0 | ||||||
|
spotSegmentation Resource Report Resource Website |
spotSegmentation (RRID:SCR_001298) | spotSegmentation | data processing software, software application, software resource, image processing software | Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three. | gridding, segmentation, microarray, preprocessing, quality control, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15845656 | Free, Available for download, Freely available | OMICS_02037 | http://www.bioconductor.org/packages/release/bioc/html/spotSegmentation.html | SCR_001298 | 2026-02-16 09:45:27 | 0 | ||||||
|
BAC Resource Report Resource Website |
BAC (RRID:SCR_001067) | BAC | software application, data processing software, sequence analysis software, data analysis software, software resource | R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments. | software, bayesian, chip, hierarchy, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00801 | SCR_001067 | 2026-02-16 09:45:24 | 0 | ||||||||
|
targetscan.Hs.eg.db Resource Report Resource Website |
targetscan.Hs.eg.db (RRID:SCR_001068) | software application, data processing software, sequence analysis software, data analysis software, software resource | R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. | software, biological targets, mirna, prediction, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00790 | SCR_001068 | 2026-02-16 09:45:24 | 0 | |||||||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | software application, data processing software, sequence analysis software, data analysis software, software resource | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-02-16 09:45:26 | 30 | ||||||
|
rGADEM Resource Report Resource Website |
rGADEM (RRID:SCR_001091) | software application, data processing software, sequence analysis software, data analysis software, software resource | R package with tools for de novo motif discovery in large-scale genomic sequence data. | de novo motif, genomics, sequencing, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00491 | SCR_001091 | 2026-02-16 09:45:24 | 0 | |||||||||
|
CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | production service resource, service resource, data analysis service, analysis service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-02-16 09:46:53 | 0 | |||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-02-16 09:45:10 | 0 | ||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-02-16 09:48:40 | 2839 | ||||||||
|
KEGGgraph Resource Report Resource Website 10+ mentions |
KEGGgraph (RRID:SCR_023788) | software resource, software toolkit | Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs. | Kyoto Encyclopedia of Genes and Genomes, KEGG, KEGG pathways, graph models, graph object, graphs visualization, | is listed by: Bioconductor | PMID:19307239 | Free, Available for download, Freely available | SCR_023788 | Kyoto Encyclopedia of Genes and Genomes graph | 2026-02-16 09:50:34 | 14 |
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