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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
featureCounts Resource Report Resource Website 10000+ mentions |
featureCounts (RRID:SCR_012919) | featureCounts | software resource | A read summarization program, which counts mapped reads for the genomic features such as genes and exons. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is required by: SL-quant |
PMID:24227677 | biotools:featurecounts, OMICS_01160 | https://bio.tools/featurecounts | SCR_012919 | featureCounts: a universal read summarization program | 2026-08-29 11:24:24 | 14312 | ||||||
|
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 | |||||||||
|
NGSmethDB Resource Report Resource Website 1+ mentions |
NGSmethDB (RRID:SCR_012847) | NGSmethDB | data or information resource, data repository, database, service resource, storage service resource | A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20965971 | OMICS_01844, biotools:ngsmethdb | https://bio.tools/ngsmethdb | SCR_012847 | NGSmethDB - A database for NGS single-cytosine-resolution DNA methylation data | 2026-08-29 11:24:23 | 9 | ||||||
|
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 | ||||||||||
|
MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | data or information resource, data repository, database, service resource, storage service resource | Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. | mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24170808 | Free, The community can contribute to this resource | biotools:mitobreak, OMICS_01640 | https://bio.tools/mitobreak | SCR_012949 | 2026-08-29 11:24:25 | 11 | ||||||
|
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 | ||||||||||
|
ArrayTrack Resource Report Resource Website 50+ mentions |
ArrayTrack (RRID:SCR_012839) | ArrayTrack | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. |
uses: Gene Ontology For Functional Analysis (GOFFA) is listed by: OMICtools has parent organization: U.S. Food and Drug Administration |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00851 | SCR_012839 | 2026-08-29 11:24:23 | 66 | |||||||||
|
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 | ||||||||||
|
RepeatMasker Resource Report Resource Website 10000+ mentions |
RepeatMasker (RRID:SCR_012954) | software resource | Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ). |
uses: Repbase uses: RMBlast is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
DOI:10.1007/978-1-61779-603-6_2 | nlx_156840, OMICS_09436 | https://sources.debian.org/src/repeatmasker/ | SCR_012954 | repeatmasker.org | 2026-08-29 11:24:25 | 10730 | ||||||||
|
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 | |||||
|
Acacia Resource Report Resource Website 100+ mentions |
Acacia (RRID:SCR_012896) | Acacia | software resource | Accurate error-correction of amplicon pyrosequences. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
DOI:10.1038/nmeth.1990 | OMICS_01116 | https://sources.debian.org/src/acacia/ | SCR_012896 | 2026-08-29 11:24:35 | 109 | ||||||||
|
TargetScore Resource Report Resource Website 1+ mentions |
TargetScore (RRID:SCR_012933) | TargetScore | software resource | Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24135265 | Free | OMICS_00421 | SCR_012933 | TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information | 2026-08-29 11:24:25 | 3 | |||||||
|
OncoSNP Resource Report Resource Website 10+ mentions |
OncoSNP (RRID:SCR_012985) | OncoSNP | software resource | An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data. | is listed by: OMICtools | Cancer | Freely available for academic use, Non-commercial, Commercial with permission | OMICS_00728 | SCR_012985 | 2026-08-29 11:24:26 | 19 | ||||||||
|
RLMM Resource Report Resource Website 1+ mentions |
RLMM (RRID:SCR_012984) | RLMM | software resource | A Genotype Calling Algorithm for Affymetrix SNP Arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00732 | SCR_012984 | 2026-08-29 11:24:25 | 5 |
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