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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | cn.farms - factor analysis for copy number estimation | 2026-10-31 12:12:36 | 0 | |||||
|
CNTools Resource Report Resource Website 1+ mentions |
CNTools (RRID:SCR_000281) | CNTools | software resource | Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data. | copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02061 | SCR_000281 | SciCrunch Registry | CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses | 2026-10-31 12:12:36 | 1 | |||||||
|
TransView Resource Report Resource Website |
TransView (RRID:SCR_000358) | TransView | software resource | Software package to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq. | rna-seq, chip-seq, clustering, dna methylation, data import, gene expression, methyl-seq, microarray, multiple comparison, sequencing, transcription, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02048 | SCR_000358 | SciCrunch Registry | 2026-10-31 12:12:37 | 0 | ||||||||
|
pvac Resource Report Resource Website |
pvac (RRID:SCR_000359) | pvac | software resource | Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC). | microarray, one channel, quality control, affymetrix, principal component analysis, 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 | biotools:pvac, OMICS_02031 | https://bio.tools/pvac | SCR_000359 | SciCrunch Registry | pvac: PCA-based gene filtering for Affymetrix arrays | 2026-10-31 12:12:37 | 0 | ||||||
|
flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | SciCrunch Registry | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-10-31 12:12:38 | 21 | |||||||
|
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 | SciCrunch Registry | OLINgui - Graphical user interface for OLIN | 2026-10-31 12:12:38 | 0 | ||||||
|
flowStats Resource Report Resource Website 1+ mentions |
flowStats (RRID:SCR_000399) | software resource | Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05611 | SCR_000399 | SciCrunch Registry | flowStats - Statistical methods for the analysis of flow cytometry data | 2026-10-31 12:12:37 | 1 | ||||||||
|
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 | SciCrunch Registry | Clonality - Clonality testing | 2026-10-31 12:12:36 | 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 | SciCrunch Registry | iBMQ - integrated Bayesian Modeling of eQTL data | 2026-10-31 12:12:39 | 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 | SciCrunch Registry | GeneExpressionSignature - Gene Expression Signature based Similarity Metric | 2026-10-31 12:12:38 | 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 | SciCrunch Registry | flowQ: Quality control for flow cytometry | 2026-10-31 12:12:40 | 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 | SciCrunch Registry | 2026-10-31 12:12:38 | 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 | SciCrunch Registry | 2026-10-31 12:12:34 | 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 | SciCrunch Registry | 2026-10-31 12:12:34 | 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 | SciCrunch Registry | VariantAnnotation - Annotation of Genetic Variants | 2026-10-31 12:12:33 | 9 | ||||||
|
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 | SciCrunch Registry | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-10-31 12:12:33 | 5 | ||||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | data analysis software, data processing software, sequence analysis software, software application, 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 | SciCrunch Registry | CorMut - Detect the correlated mutations based on selection pressure | 2026-10-31 12:12:32 | 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 |
Canadian Cancer Society ; International Society for the Advancement of Cytometry ; Michael Smith Foundation for Health Research ; NIBIB R01EB008400 |
PMID:25600947 | Free, Available for download, Freely available | OMICS_05593 | SCR_000051 | SciCrunch Registry | flowBin - Combining multitube flow cytometry data by binning | 2026-10-31 12:12:32 | 0 | ||||||
|
metaSeq Resource Report Resource Website |
metaSeq (RRID:SCR_000056) | metaSeq | data analysis software, data processing software, software application, software resource | Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method. | differential expression, rna-seq, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02123 | SCR_000056 | SciCrunch Registry | 2026-10-31 12:12:32 | 0 | ||||||||
|
CGHnormaliter Resource Report Resource Website 1+ mentions |
CGHnormaliter (RRID:SCR_002936) | software resource | Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). | standalone software, mac os x, unix/linux, windows, r, array comparative genomic hybridization, copy number alteration, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20418341 | Free, Available for download, Freely available | OMICS_02572 | http://www.bioconductor.org/packages/release/bioc/html/CGHnormaliter.html | SCR_002936 | SciCrunch Registry | CGHnormaliter - Normalization of array CGH data with imbalanced aberrations. | 2026-10-31 12:13:14 | 2 |
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