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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GSVA Resource Report Resource Website 100+ mentions |
GSVA (RRID:SCR_021058) | GSVA | data processing software, data analysis software, software resource, software application, software toolkit | Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner. | Gene set enrichment, variation estimation, pathway activity, sample population, microarray, RNA-seq, data analysis | is listed by: Bioconductor | ISCIII COMBIOMED ; Spanish MINECO ; NCI U54 CA149237 |
PMID:23323831 | Free, Available for download, Freely available | SCR_021058 | Gene Set Variation Analysis | 2026-08-04 09:44:42 | 256 | ||||||
|
epialleleR Resource Report Resource Website 1+ mentions |
epialleleR (RRID:SCR_023913) | software resource, software toolkit | Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data. | BAM files, binary alignment map files, allele specific methylation analysis, methylation sequencing data, next generation sequencing data, hypermethylated variant epiallele frequencies calling, | is listed by: Bioconductor | K.G.Jebsen Foundation ; Norwegian Cancer Society ; Norwegian Research Council |
DOI:10.1101/2022.06.30.498213 | Free, Available for download, Freely available | https://github.com/BBCG/epialleleR | SCR_023913 | 2026-08-04 09:45:22 | 1 | |||||||
|
SimFFPE Resource Report Resource Website 1+ mentions |
SimFFPE (RRID:SCR_021085) | simulation software, software application, software resource | Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls. | FFPE, NGS read simulator, artifact chimeric read, next generation sequencing process, normal reads simulation, artifact chimeric reads simulation, formalin fixed paraffin embedded tissue, |
is listed by: Bioconductor is related to: CRAN |
Free, Available for download, Freely available | SCR_021085 | NGS Read Simulator for FFPE Tissue, Simulator for FFPE Tissue | 2026-08-04 09:44:43 | 1 | |||||||||
|
PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | data processing software, data analysis software, software resource, software application, software toolkit | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-08-04 09:44:47 | 8 | ||||||
|
svaNUMT Resource Report Resource Website 1+ mentions |
svaNUMT (RRID:SCR_021381) | data processing software, software application, software resource, data analysis software | Software R package for Nuclear Mitochondrial integration events NUMT detection using structural variant calls. | Nuclear mitochondrial integration events, NUMT, NUMT detection, structural variant calls. | is listed by: Bioconductor | Free, Available for download, Freely available | https://bioconductor.org/packages/svaNUMT/ | SCR_021381 | 2026-08-04 09:44:48 | 1 | |||||||||
|
PICS Resource Report Resource Website 1+ mentions |
PICS (RRID:SCR_001093) | data processing software, data analysis software, software resource, sequence analysis software, software application | R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach. | chip seq, bayes, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20528864 | Free, Available for download, Freely available | OMICS_00455 | SCR_001093 | Probabilistic inference of ChIP-seq | 2026-08-04 09:40:18 | 3 | |||||||
|
Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data processing software, software application, software resource, data or information resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind | SCR_017339 | 2026-08-04 09:44:09 | 1 | |||||||||
|
CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | data analysis service, analysis service resource, production service resource, 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 | 2026-08-04 09:41:45 | 0 | |||
|
BHC Resource Report Resource Website |
BHC (RRID:SCR_006399) | BHC | data processing software, software application, software resource | Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets. | clustering, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19660130 | GNU General Public License, v3 | OMICS_02215 | SCR_006399 | Bayesian Hierarchical Clustering | 2026-08-04 09:41:35 | 0 | ||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, standalone software, software resource | 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 | 2026-08-04 09:40:02 | 0 | ||||||
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GeneNetworkBuilder Resource Report Resource Website 1+ mentions |
GeneNetworkBuilder (RRID:SCR_006455) | GeneNetworkBuilder | software application, software resource | Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF. | transcription factor, graph, network, microarray, sequencing, chip-chip, chip-seq, gene expression, regulatory network, target |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00806, OMICS_01971 | http://www.bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html | SCR_006455 | GeneNetworkBuilder - Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data | 2026-08-04 09:41:37 | 2 | ||||||
|
Orthology.eg.db Resource Report Resource Website 1+ mentions |
Orthology.eg.db (RRID:SCR_024740) | software resource, software toolkit | 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 | 2026-08-04 09:45:35 | 1 | ||||||||||
|
ExperimentHub Resource Report Resource Website 1+ mentions |
ExperimentHub (RRID:SCR_024820) | software resource, software toolkit | 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 | 2026-08-04 09:45:36 | 2 |
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