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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, data processing software, software application, software resource | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-29 11:24:00 | 27197 | ||||||
|
DNAcopy Resource Report Resource Website 100+ mentions |
DNAcopy (RRID:SCR_012560) | DNAcopy | software resource | Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
OMICS_00720, biotools:dnacopy | https://bio.tools/dnacopy, https://sources.debian.org/src/r-bioc-dnacopy/ | SCR_012560 | 2026-08-29 11:24:20 | 349 | ||||||||
|
ExiMiR Resource Report Resource Website 1+ mentions |
ExiMiR (RRID:SCR_012753) | ExiMiR | software resource | R functions for the normalization of Exiqon miRNA array data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00783 | SCR_012753 | 2026-08-29 11:24:22 | 1 | ||||||||||
|
motifRG Resource Report Resource Website 1+ mentions |
motifRG (RRID:SCR_012602) | motifRG | software resource | Software tools for discriminative motif discovery using regression methods. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24162561 | Free | OMICS_00487 | SCR_012602 | motifRG - A package for discriminative motif discovery designed for high throughput sequencing dataset | 2026-08-29 11:24:20 | 5 | |||||||
|
MiRaGE Resource Report Resource Website 10+ mentions |
MiRaGE (RRID:SCR_012738) | MiRaGE | software resource | Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00785 | SCR_012738 | 2026-08-29 11:24:21 | 33 | ||||||||||
|
CexoR Resource Report Resource Website |
CexoR (RRID:SCR_012769) | CexoR | software resource | Software for strand specific peak-pair calling in ChIP-exo replicates. |
is listed by: OMICtools has parent organization: Bioconductor |
MIT License | OMICS_00519 | SCR_012769 | CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates | 2026-08-29 11:24:32 | 0 | ||||||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data analysis software, data processing software, software application, software resource | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
Harris and IBS Honours scholarships ; Independent Research Institutes Infrastructure Support Scheme 361646; Melbourne International Research Scholarship ; NHMRC 406657; Victorian State Government OIS grant |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-08-29 11:24:34 | 23868 | ||||
|
tRanslatome Resource Report Resource Website 1+ mentions |
tRanslatome (RRID:SCR_012810) | tRanslatome | software resource | Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24222209 | Free | OMICS_01316 | SCR_012810 | tRanslatome - Comparison between multiple levels of gene expression | 2026-08-29 11:24:34 | 2 | |||||||
|
Bioconductor mailing list Resource Report Resource Website 1+ mentions |
Bioconductor mailing list (RRID:SCR_012915) | Bioconductor mailing list | data or information resource, feed, listserv, narrative resource | This mailing list is for announcements about Bioconductor and the availability of new code and questions and answers about problems and solutions using Bioconductor. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01705 | SCR_012915 | 2026-08-29 11:24:24 | 2 | ||||||||||
|
BicARE Resource Report Resource Website |
BicARE (RRID:SCR_012881) | BicARE | software resource | Biclustering Analysis and Results Exploration. |
is listed by: OMICtools has parent organization: Bioconductor |
Free | OMICS_01803 | SCR_012881 | 2026-08-29 11:24:23 | 0 | |||||||||
|
dmrFinder Resource Report Resource Website 10+ mentions |
dmrFinder (RRID:SCR_012853) | dmrFinder | software resource | Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00621 | SCR_012853 | 2026-08-29 11:24:23 | 29 | ||||||||||
|
ChIPpeakAnno Resource Report Resource Website 100+ mentions |
ChIPpeakAnno (RRID:SCR_012828) | ChIPpeakAnno | software resource | Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00804 | SCR_012828 | 2026-08-29 11:24:34 | 480 | ||||||||||
|
inSilicoMerging Resource Report Resource Website 10+ mentions |
inSilicoMerging (RRID:SCR_012829) | inSilicoMerging | software resource | Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00859 | SCR_012829 | 2026-08-29 11:24:23 | 41 | ||||||||||
|
DEXSeq Resource Report Resource Website 500+ mentions |
DEXSeq (RRID:SCR_012823) | DEXSeq | software resource | Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
OMICS_01329, biotools:dexseq | https://bio.tools/dexseq | SCR_012823 | 2026-08-29 11:24:22 | 540 | ||||||||
|
snapCGH Resource Report Resource Website 1+ mentions |
snapCGH (RRID:SCR_012947) | snapCGH | software resource | Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00734 | SCR_012947 | 2026-08-29 11:24:35 | 5 | ||||||||||
|
minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data analysis software, data processing software, data visualization software, software application, software resource | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-08-29 11:24:22 | 417 | ||||||
|
miRNApath Resource Report Resource Website 1+ mentions |
miRNApath (RRID:SCR_012833) | miRNApath | software resource | Software package that provides pathway enrichment techniques for miRNA expression data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00787 | SCR_012833 | 2026-08-29 11:24:22 | 5 | ||||||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, data processing software, software application, software resource | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-29 11:24:23 | 3073 | ||||
|
sva package Resource Report Resource Website 100+ mentions |
sva package (RRID:SCR_012836) | sva package | software resource | Contains functions for removing batch effects and other unwanted variation in high-throughput experiment. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00861 | SCR_012836 | Surrogate Variable Analysis | 2026-08-29 11:24:22 | 100 | |||||||||
|
DNaseR Resource Report Resource Website |
DNaseR (RRID:SCR_012819) | DNaseR | software resource | A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23118738 | Free | biotools:dnaser, OMICS_00517 | https://bio.tools/dnaser | SCR_012819 | DNaseR: DNase I footprinting analysis of DNase-seq data | 2026-08-29 11:24:22 | 0 |
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