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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Clonality Resource Report Resource Website |
Clonality (RRID:SCR_000293) | Clonality | software resource | Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles. | classification, copy number variant, microarray, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02059 | SCR_000293 | Clonality - Clonality testing | 2026-02-14 01:59:41 | 0 | |||||||
|
iBMQ Resource Report Resource Website |
iBMQ (RRID:SCR_000481) | software resource | Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently. | standalone software, mac os x, unix/linux, windows, r, gene expression, microarray, preprocessing, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23958729 | Free, Available for download, Freely available | OMICS_04601 | SCR_000481 | iBMQ - integrated Bayesian Modeling of eQTL data | 2026-02-14 01:59:45 | 0 | |||||||
|
OLINgui Resource Report Resource Website |
OLINgui (RRID:SCR_000435) | OLINgui | software resource | Software package providing a graphical user interface for the OLIN package. | microarray, preprocessing, quality control, two channel, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | BioTools:olingui, OMICS_02030 | https://bio.tools/olingui | SCR_000435 | OLINgui - Graphical user interface for OLIN | 2026-02-14 01:59:43 | 0 | ||||||
|
GeneExpressionSignature Resource Report Resource Website 1+ mentions |
GeneExpressionSignature (RRID:SCR_000455) | software resource | An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest. | software package, r, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23374109 | Free, Available for download, Freely available | OMICS_04919 | SCR_000455 | GeneExpressionSignature - Gene Expression Signature based Similarity Metric | 2026-02-14 01:59:46 | 1 | |||||||
|
flowQ Resource Report Resource Website |
flowQ (RRID:SCR_000575) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05805 | SCR_000575 | flowQ: Quality control for flow cytometry | 2026-02-14 01:59:46 | 0 | ||||||||
|
SigFuge Resource Report Resource Website |
SigFuge (RRID:SCR_000444) | software resource | Algorithm for testing significance of clustering in RNA-seq data. | software package, unix/linux, mac os x, windows, r, clustering, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25030904 | Free, Available for download, Freely available | OMICS_05201 | SCR_000444 | 2026-02-14 01:59:44 | 0 | ||||||||
|
ArrayExpress (R) Resource Report Resource Website 1+ mentions |
ArrayExpress (R) (RRID:SCR_000120) | ArrayExpress (R) | software resource | Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet | microarray |
is listed by: OMICtools is related to: ArrayExpress has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:19505942 | Free, Available for download, Freely available | OMICS_01974 | SCR_000120 | 2026-02-14 01:59:37 | 1 | |||||||
|
AffyRNADegradation Resource Report Resource Website |
AffyRNADegradation (RRID:SCR_000118) | AffyRNADegradation | software resource | Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation. | rna degradation, gene expression, microarray, preprocessing, affymetrix, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: University of Leipzig; Saxony; Germany |
PMID:23097420 | Free, Available for download, Freely available | OMICS_01975, biotools:affyrnadegradation | https://bio.tools/affyrnadegradation | SCR_000118 | 2026-02-14 01:59:37 | 0 | ||||||
|
VariantAnnotation Resource Report Resource Website 1+ mentions |
VariantAnnotation (RRID:SCR_000074) | VariantAnnotation | software resource | Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes. | annotation, genetic variant, data import, genetics, high throughput sequencing, snp, sequencing |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor has parent organization: Fred Hutchinson Cancer Center |
PMID:24681907 | Free, Available for download, Freely available | OMICS_02073 | SCR_000074 | VariantAnnotation - Annotation of Genetic Variants | 2026-02-14 01:59:36 | 8 | ||||||
|
timecourse Resource Report Resource Website 1+ mentions |
timecourse (RRID:SCR_000077) | timecourse | software resource | Software functions for data analysis and graphical displays for developmental microarray time course data. | microarray, differential expression, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: CRAN has parent organization: Bioconductor has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | OMICS_01980, biotools:timecourse | https://bio.tools/timecourse | SCR_000077 | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-02-14 01:59:36 | 5 | ||||||
|
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 | ncdfFlow: A package that provides ncdf based storage for flow cytometry data | 2026-02-14 01:59:34 | 0 | ||||||||
|
flowBin Resource Report Resource Website |
flowBin (RRID:SCR_000051) | software resource | A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers. | software package, flow cytometry data, r, cell based assay, expression |
is related to: CRAN has parent organization: Bioconductor has parent organization: BC Cancer Agency |
NIBIB R01EB008400; Canadian Cancer Society ; Michael Smith Foundation for Health Research ; International Society for the Advancement of Cytometry |
PMID:25600947 | Free, Available for download, Freely available | OMICS_05593 | SCR_000051 | flowBin - Combining multitube flow cytometry data by binning | 2026-02-14 01:59:35 | 0 | ||||||
|
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 |
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 | 2026-02-14 02:05:29 | 10 | ||||||||
|
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 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-02-14 02:04:50 | 0 | ||||||
|
svaNUMT Resource Report Resource Website 1+ mentions |
svaNUMT (RRID:SCR_021381) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:02 | 1 | |||||||||
|
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 | 2026-02-15 09:19:28 | 2 | ||||||
|
epialleleR Resource Report Resource Website 1+ mentions |
epialleleR (RRID:SCR_023913) | software toolkit, software resource | 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 | 2026-02-15 09:23:28 | 1 | |||||||
|
factDesign Resource Report Resource Website |
factDesign (RRID:SCR_001330) | factDesign | software application, data processing software, data analysis software, software resource | Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. | microarray, differential expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18584033 | Free, Available for download, Freely available | OMICS_02008 | SCR_001330 | factDesign - Factorial designed microarray experiment analysis | 2026-02-15 09:18:05 | 0 | ||||||
|
pickgene Resource Report Resource Website |
pickgene (RRID:SCR_001331) | pickgene | software application, data processing software, data analysis software, software resource | Software for adaptive Gene Picking for Microarray Expression Data Analysis. | microarray, gene expression, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02007, biotools:pickgene | https://bio.tools/pickgene | SCR_001331 | 2026-02-15 09:18:05 | 0 | |||||||
|
GeneMeta Resource Report Resource Website 1+ mentions |
GeneMeta (RRID:SCR_001201) | GeneMeta | software application, data processing software, data analysis software, software resource | Software package providing a collection of meta-analysis tools for analysing high throughput experimental data. | sequencing, high throughput |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02120 | SCR_001201 | GeneMeta - MetaAnalysis for High Throughput Experiments | 2026-02-15 09:18:03 | 1 |
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