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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | analysis service resource, data analysis service, 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 | SciCrunch Registry | Chinese Restaurant ClusterView | 2026-10-24 12:50:42 | 0 | |||
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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 | SciCrunch Registry | Kyoto Encyclopedia of Genes and Genomes graph | 2026-10-24 12:51:58 | 15 | ||||||||
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Fred Hutchinson Cancer Center Resource Report Resource Website 10+ mentions |
Fred Hutchinson Cancer Center (RRID:SCR_004984) | Fred Hutch Cancer Research Center | institution | Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance (SCCA) have merged to form Fred Hutchinson Cancer Center, unified adult cancer research and care center. Independent, nonprofit organization is clinically integrated part of UW Medicine and is UW Medicine’s cancer program. | Adult cancer research and care center, UW Medicine, cancer |
is parent organization of: CODEHOP is parent organization of: Coddle-Codons Optimized to Discover Deleterious LEsions is parent organization of: Pplacer is parent organization of: International Histocompatibility Cell and DNA Bank is parent organization of: Bioconductor is parent organization of: Blocks is parent organization of: VariantAnnotation is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Proteomics Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Research Freezers and Sample Storage Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Flow Cytometry is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Specimen Processing/Research Cell Bank is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Glassware Services is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Electron Microscopy is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Experimental Histopathology Shared Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Arnold Library is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Genomics Shared Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Comparative Medicine is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Antibody Technology is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology is parent organization of: Fred Hutchinson Cancer Center Therapeutic Products Core Facility is parent organization of: Fred Hutchinson Cancer Center Prevention Center Shared Resource Core Facility is parent organization of: Fred Hutchinson Cancer Center Biostatistics Shared Resource is parent organization of: Fred Hutchinson Cancer Center Collaborative Data Services Core Facility is parent organization of: Fred Hutchinson Cancer Center Genomics and Bioinformatics Core Facility is parent organization of: Fred Hutchinson Cancer Center Antibody Technology Core Facility is parent organization of: Fred Hutchinson Cancer Center Cellular Imaging Core Facility is parent organization of: Fred Hutchinson Cancer Center Comparative Medicine Core Facility is parent organization of: Fred Hutchinson Cancer Center Electron Microscopy Core Facility is parent organization of: Fred Hutchinson Cancer Center Experimental Histopathology Core Facility is parent organization of: Fred Hutchinson Cancer Center Flow Cytometry Core Facility is parent organization of: Fred Hutchinson Cancer Center Immune Monitoring Core Facility is parent organization of: Fred Hutchinson Cancer Center Preclinical Imaging Core Facility is parent organization of: Fred Hutchinson Cancer Center Preclinical Modeling Core Facility is parent organization of: Fred Hutchinson Cancer Center Proteomics and Metabolomics Core Facility is parent organization of: Fred Hutchinson Cancer Center Leica Center of Excellence Core Facility is parent organization of: Fred Hutch Cancer Center Translational Pathology Core Facility |
Wikidata Q1452369, , Crossref Funder ID 100005895, ISNI 0000 0001 2180 1622, nlx_94018, GRID grid.270240.3 | https://ror.org/007ps6h72, https://www.fhcc.org/?_gl=1%2A1ewelpw%2A_ga%2AMTY0NDY4MTI0LjE2NTg5NDc1OTQ.%2A_ga_CMZTF4L2MS%2AMTY1ODk0NzU5NC4xLjEuMTY1ODk0ODUyNy4w | SCR_004984 | SciCrunch Registry | 2026-10-24 12:49:51 | 10 | ||||||||
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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 | SciCrunch Registry | Bayesian Hierarchical Clustering | 2026-10-24 12:49:52 | 0 | ||||||
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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 | SciCrunch Registry | ReadqPCR - Read qPCR data | 2026-10-24 12:51:17 | 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 | SciCrunch Registry | GeneNetworkBuilder - Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data | 2026-10-24 12:51:28 | 2 | ||||||
|
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 | SciCrunch Registry | 2026-10-24 12:51:45 | 3080 | ||||||||
|
AUCell Resource Report Resource Website 50+ mentions |
AUCell (RRID:SCR_021327) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package to identify cells with active gene sets in single cell RNA-seq data. Used for analysis of gene set activity in single cell RNA-seq data.Used to calculate whether critical subset of input gene set is enriched within expressed genes for each cell. | Identify cells with active gene sets, single cell RNA-seq data, gene set activity analysis | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_021327 | SciCrunch Registry | Area Under the Curve | 2026-10-24 12:49:16 | 56 | |||||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | SciCrunch Registry | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-10-24 12:49:25 | 0 | ||||||
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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 | SciCrunch Registry | 2026-10-24 12:50:09 | 1 | |||||||
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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 | SciCrunch Registry | 2026-10-24 12:53:22 | 1 | ||||||||||
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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 | SciCrunch Registry | 2026-10-24 12:53:24 | 2 | ||||||||||
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ncdfFlow Resource Report Resource Website |
ncdfFlow (RRID:SCR_000009) | software resource | Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05617 | SCR_000009 | SciCrunch Registry | ncdfFlow: A package that provides ncdf based storage for flow cytometry data | 2026-10-24 12:54:53 | 0 |
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