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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 | 2026-08-29 11:20:29 | 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 | 2026-08-29 11:20:38 | 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 | 2026-08-29 11:20:25 | 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 | 2026-08-29 11:20:25 | 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 | 2026-08-29 11:20:27 | 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 | 2026-08-29 11:20:25 | 0 | ||||||||
|
easyRNASeq Resource Report Resource Website 10+ mentions |
easyRNASeq (RRID:SCR_012020) | easyRNASeq | software resource | Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package. | rna-seq, gene expression, genetics, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Molecular Biology Laboratory |
PMID:22847932 | Artistic License, v2 | OMICS_01938, biotools:easyrnaseq | https://bio.tools/easyrnaseq | SCR_012020 | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-08-29 11:24:10 | 30 | |||||
|
LVSmiRNA Resource Report Resource Website |
LVSmiRNA (RRID:SCR_012752) | LVSmiRNA | software resource | Software for normalization of Agilent miRNA arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00784 | SCR_012752 | 2026-08-29 11:24:32 | 0 | ||||||||||
|
MMDiff Resource Report Resource Website 1+ mentions |
MMDiff (RRID:SCR_012692) | MMDiff | software resource | Software package that detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples. |
is listed by: OMICtools has parent organization: Bioconductor |
Free | OMICS_00474 | SCR_012692 | MMDiff - Statistical Testing for ChIP-Seq data sets | 2026-08-29 11:24:31 | 8 | ||||||||
|
CRLMM Resource Report Resource Website 10+ mentions |
CRLMM (RRID:SCR_012580) | CRLMM | software resource | Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00717 | SCR_012580 | 2026-08-29 11:24:18 | 10 | ||||||||||
|
baySeq Resource Report Resource Website 100+ mentions |
baySeq (RRID:SCR_012795) | baySeq | software resource | Software package that identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20698981 | OMICS_01299 | SCR_012795 | 2026-08-29 11:24:21 | 121 | |||||||||
|
RPA Resource Report Resource Website 1+ mentions |
RPA (RRID:SCR_012768) | RPA | software resource | A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00778 | SCR_012768 | RPA: Robust Probabilistic Averaging for probe-level analysis | 2026-08-29 11:24:21 | 1 | |||||||||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-08-29 11:24:21 | 319 | ||||||||
|
rqubic Resource Report Resource Website |
rqubic (RRID:SCR_012869) | rqubic | software resource | This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19509312 | Free | biotools:rqubic, OMICS_01799 | https://bio.tools/rqubic | SCR_012869 | rqubic - Qualitative biclustering algorithm for expression data analysis in R | 2026-08-29 11:24:34 | 0 | |||||
|
DiffBind Resource Report Resource Website 1000+ mentions |
DiffBind (RRID:SCR_012918) | DiffBind | software resource | Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
biotools:diffbind, OMICS_00471 | https://bio.tools/diffbind | SCR_012918 | Differential Binding Analysis of ChIP-Seq peak data | 2026-08-29 11:24:35 | 1449 | |||||||
|
iBBiG Resource Report Resource Website 1+ mentions |
iBBiG (RRID:SCR_012882) | iBBiG | software resource | A bi-clustering algorithm which is optimizes for binary data analysis. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22789589 | Free | OMICS_01802 | SCR_012882 | Iterative Binary Biclustering of Genesets | 2026-08-29 11:24:34 | 3 | |||||||
|
eisa Resource Report Resource Website 1+ mentions |
eisa (RRID:SCR_012883) | eisa | software resource | A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free | OMICS_01801, biotools:eisa | https://bio.tools/eisa | SCR_012883 | eisa - Expression data analysis via the Iterative Signature Algorithm | 2026-08-29 11:24:23 | 2 | ||||||
|
Methylumi Resource Report Resource Website 10+ mentions |
Methylumi (RRID:SCR_012831) | Methylumi | software resource | Software package that provides classes for holding and manipulating Illumina methylation data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00798 | SCR_012831 | 2026-08-29 11:24:34 | 23 | ||||||||||
|
iChip Resource Report Resource Website 10+ mentions |
iChip (RRID:SCR_012958) | iChip | software resource | Software package that uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00807 | SCR_012958 | 2026-08-29 11:24:25 | 33 | ||||||||||
|
NarrowPeaks Resource Report Resource Website 10+ mentions |
NarrowPeaks (RRID:SCR_012924) | NarrowPeaks | software resource | Software package for post-processing of peaks and differential binding in ChIP-seq based on standard wiggle visualization files. The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process data in wiggle track format (WIG) commonly produced by ChIP-seq peak finders by applying FPCA over a set of selected candidate enriched regions. This is done in order to shorten the genomic locations accounting for a given proportion of variation among the enrichment-score profiles. The function ''narrowpeaks'' allows the user to discriminate between binding regions in close proximity to each other and to narrow down the length of the putative transcription factor binding sites while preserving the information present in the variability of the dataset and capturing major sources of variation. (2) Analyze differential variation when multiple ChIP-seq samples need to compared. The function ''narrowpeaksDiff'' quantifies differences between the tag-enrichment, and uses non-parametric tests on the FPC scores for testing differences between conditions. | functional principal component analysis |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License | OMICS_00449 | SCR_012924 | NarrowPeaks: Analysis of Variation in ChIP-seq using Functional PCA Statistics | 2026-08-29 11:24:24 | 49 |
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