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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-12 12:57:53 | 0 | |||||
|
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 | 2026-09-12 12:57:53 | 2 | |||||||
|
BEDOPS Resource Report Resource Website 100+ mentions |
BEDOPS (RRID:SCR_012865) | BEDOPS | software resource | A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets. |
is listed by: OMICtools is listed by: Debian |
PMID:22576172 DOI:10.1093/bioinformatics/bts277 |
GNU General Public License, v3 | OMICS_00949 | https://sources.debian.org/src/bedops/ | SCR_012865 | BEDOPS: high-performance genomic feature operations | 2026-09-12 12:57:54 | 237 | ||||||
|
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 | 2026-09-12 12:57:55 | 2 | ||||||||||
|
NCBI Assembly Archive Viewer Resource Report Resource Website 100+ mentions |
NCBI Assembly Archive Viewer (RRID:SCR_012917) | NCBI Assembly Archive Viewer | data or information resource, data repository, data set, service resource, storage service resource | Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). | sequence alignment, sequence chromatogram, assembly, virus |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is related to: GenBank is related to: Trace Archive is related to: DNA DataBank of Japan (DDBJ) is related to: European Nucleotide Archive (ENA) |
OMICS_00890, r3d100012688 | http://www.ncbi.nlm.nih.gov/assembly, https://doi.org/10.17616/R31NJMA8 | http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi | SCR_012917 | Assembly Archive Viewer, NCBI Assembly, Assembly | 2026-09-12 12:57:55 | 313 | ||||||
|
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 | 2026-09-12 12:57:55 | 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 | 2026-09-12 12:57:54 | 0 | |||||||||
|
CloudAligner Resource Report Resource Website 1+ mentions |
CloudAligner (RRID:SCR_012962) | CloudAligner | software resource | A map/reduce based application for mapping short reads generated by the next-generation sequencing machines. | matlab, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21645377 | GNU General Public License, v3 | OMICS_00656, biotools:cloudaligner | https://bio.tools/cloudaligner | SCR_012962 | 2026-09-12 12:57:56 | 4 | ||||||
|
InCroMAP Resource Report Resource Website 10+ mentions |
InCroMAP (RRID:SCR_012964) | InCroMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data. | is listed by: OMICtools | PMID:23257199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00855 | SCR_012964 | 2026-09-12 12:57:56 | 11 | ||||||||
|
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 | 2026-09-12 12:57:54 | 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 | 2026-09-12 12:57:54 | 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 | 2026-09-12 12:57:53 | 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 | 2026-09-12 12:57:56 | 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 | 2026-09-12 12:57:53 | 41 | ||||||||||
|
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 | 2026-09-12 12:57:56 | 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 | 2026-09-12 12:57:53 | 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 | 2026-09-12 12:57:53 | 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 | 2026-09-12 12:57:53 | 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 | 2026-09-12 12:57:56 | 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 | 2026-09-12 12:57:53 | 3073 |
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