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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NEXT-peak Resource Report Resource Website 1+ mentions |
NEXT-peak (RRID:SCR_010862) | NEXT-peak | software resource | A software program to call peaks from ChIP-seq data for transcription factor binding sites. |
is listed by: OMICtools has parent organization: Old Dominion University; Virginia; USA |
PMID:23706083 | OMICS_00450 | SCR_010862 | 2026-08-01 12:04:18 | 1 | |||||||||
|
PeakRanger Resource Report Resource Website 10+ mentions |
PeakRanger (RRID:SCR_010863) | PeakRanger | software resource | Software for a multi-purpose ChIP Seq peak caller. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21554709 | OMICS_00451, biotools:peakranger | https://bio.tools/peakranger | SCR_010863 | 2026-08-01 12:03:59 | 21 | |||||||
|
RRBSMAP Resource Report Resource Website 1+ mentions |
RRBSMAP (RRID:SCR_010864) | RRBSMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS). |
is listed by: OMICtools has parent organization: Google Code |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00589 | SCR_010864 | 2026-08-01 12:04:17 | 5 | |||||||||
|
SIPeS Resource Report Resource Website 1+ mentions |
SIPeS (RRID:SCR_010865) | SIPeS | software resource | An algorithm that allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity. | is listed by: OMICtools | PMID:20144209 | Free to academic users, Non-commercial, Commercial requires permission | OMICS_00462 | SCR_010865 | SIPeS - Site Identification from Paired-end Sequencing, Site Identification from Paired-end Sequencing | 2026-08-01 12:04:18 | 5 | |||||||
|
T-PIC Resource Report Resource Website 1+ mentions |
T-PIC (RRID:SCR_010867) | T-PIC | software resource | A software for determining DNA/protein binding sites from a ChIP-Seq experiment. |
is listed by: OMICtools has parent organization: University of Miami; Florida; USA |
OMICS_00464 | SCR_010867 | 2026-08-01 12:04:17 | 7 | ||||||||||
|
SEAL Resource Report Resource Website 100+ mentions |
SEAL (RRID:SCR_010914) | SEAL | software resource | A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21697132 | biotools:seal, OMICS_00682 | https://bio.tools/seal | SCR_010914 | 2026-08-01 12:04:01 | 121 | |||||||
|
aCGHtool Resource Report Resource Website 1+ mentions |
aCGHtool (RRID:SCR_010915) | aCGHtool | software resource | A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs. | is listed by: OMICtools | OMICS_00699 | SCR_010915 | 2026-08-01 12:04:18 | 1 | ||||||||||
|
Agilent Genomic Workbench Resource Report Resource Website 100+ mentions |
Agilent Genomic Workbench (RRID:SCR_010918) | Agilent Genomic Workbench | software resource | A comprehensive design and analysis tool for setting up and interpreting your microarray experiments. | is listed by: OMICtools | OMICS_00702 | SCR_010918 | 2026-08-01 12:04:18 | 248 | ||||||||||
|
DBChIP Resource Report Resource Website 1+ mentions |
DBChIP (RRID:SCR_010872) | DBChIP | software resource | Detects differential binding of transcription factors with ChIP-seq. | is listed by: OMICtools | OMICS_00470 | SCR_010872 | 2026-08-01 12:03:59 | 5 | ||||||||||
|
DIME Resource Report Resource Website 10+ mentions |
DIME (RRID:SCR_010874) | DIME | software resource | R-package for identifying differential ChIP-seq based on an ensemble of mixture models. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:DIME, OMICS_00473 | https://bio.tools/DIME | SCR_010874 | 2026-08-01 12:04:18 | 29 | ||||||||
|
ChIPModule Resource Report Resource Website 1+ mentions |
ChIPModule (RRID:SCR_010877) | ChIPModule | software resource | A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data. | is listed by: OMICtools | OMICS_00477 | SCR_010877 | ChIPModule: Systematic discovery of transcription factors and their cofactors from ChIP-seq data | 2026-08-01 12:04:18 | 1 | |||||||||
|
ERNE Resource Report Resource Website 10+ mentions |
ERNE (RRID:SCR_010912) | ERNE | software resource | A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00662 | SCR_010912 | 2026-08-01 12:04:18 | 46 | ||||||||||
|
F-Seq Resource Report Resource Website 50+ mentions |
F-Seq (RRID:SCR_010880) | F-Seq | software resource | A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser. |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00482 | SCR_010880 | 2026-08-01 12:04:17 | 83 | ||||||||||
|
Aldevron Resource Report Resource Website 10+ mentions |
Aldevron (RRID:SCR_011017) | Aldevron | commercial organization | Contract manufacturing services company, specializing in plasmid DNA manufacturing, protein services and antibody development.Producesg high quality plasmid DNA, proteins, enzymes, antibodies, and other biologicals in support of clients objectives. | is listed by: ScienceExchange | SciEx_9447 | http://www.scienceexchange.com/facilities/aldevron | SCR_011017 | 2026-08-01 12:04:19 | 46 | |||||||||
|
Medical Research Council Resource Report Resource Website 10+ mentions |
Medical Research Council (RRID:SCR_011018) | MRC, UK MRC | institution | The Medical Research Council is a publicly-funded organization dedicated to improving human health. We support research across the entire spectrum of medical sciences, in universities and hospitals, in our own units, centers and institutes in the UK, and in our units in Africa. | is related to: EMIF | Wikidata: Q746879, Crossref funder ID: 501100000265, nlx_inv_1005080, ISNI: 122478951, grid.14105.31 | https://ror.org/03x94j517 | SCR_011018 | UK Medical Research Council, British Medical Research Council | 2026-08-01 12:04:19 | 18 | ||||||||
|
Mouse Clinical Institute; Alsace; France Resource Report Resource Website 10+ mentions |
Mouse Clinical Institute; Alsace; France (RRID:SCR_011021) | MCI, ICS | institution | Research infrastructure for generation of new mouse models,being therefore the most important transgenic mouse production unit in France. | is related to: AgedBrainSYSBIO | nlx_158126, ISNI: 0000 0004 0404 8159, grid.452426.3 | https://ror.org/03cjqqq10 | SCR_011021 | Mouse Clinical Institute, Institut Clinique de la Souris, Institut Clinique de la Souris; Alsace; France | 2026-08-01 12:04:19 | 10 | ||||||||
|
Cayetano Heredia University; Lima; Peru Resource Report Resource Website 10+ mentions |
Cayetano Heredia University; Lima; Peru (RRID:SCR_011142) | university | Private nonprofit university located in Lima, Peru. It was named in honor of Cayetano Heredia, one of the eminent Peruvian physicians of the 19th century. The university is overseen by a board of trustees and is not owned by any private or state entity. | is parent organization of: CELL- PREVEN Project | nlx_71545 | http://www.upch.edu.pe/ | SCR_011142 | UPCH | 2026-08-01 12:04:21 | 33 | |||||||||
|
Chang Gung University; Taoyuan; Taiwan Resource Report Resource Website 1+ mentions |
Chang Gung University; Taoyuan; Taiwan (RRID:SCR_011149) | CGU | university | Chang Gung University is a private university in Guishan District, Taoyuan City, Taiwan. | is parent organization of: Chang Gung University College of Medicine; Taoyuan; Taiwan | nlx_157707 | SCR_011149 | Chang Gung University | 2026-08-01 12:04:21 | 1 | |||||||||
|
Baylor University; Texas; USA Resource Report Resource Website 1+ mentions |
Baylor University; Texas; USA (RRID:SCR_011029) | university | Private Baptist research university in Waco, Texas. Baylor was chartered in 1845 by the last Congress of the Republic of Texas. |
is parent organization of: Baylor University Department of Psychology and Neuroscience is parent organization of: Baylor College of Medicine - Shaw Laboratory is parent organization of: Genboree Discovery System is parent organization of: National Center for Macromolecular Imaging is parent organization of: Sea Urchin Genome Project is parent organization of: Sea Urchin Genome Project is parent organization of: Tribolium castaneum Genome Project is parent organization of: Honey Bee Genome Project is parent organization of: EMDataResource.org is parent organization of: BCM Department of Neuroscience Andreas Tolias Lab is parent organization of: HapMap 3 and ENCODE 3 is parent organization of: SimRare is parent organization of: PhenoMan is parent organization of: Human Epigenome Atlas is parent organization of: Baylor College of Medicine; Department of Pharmacology is parent organization of: Baylor College of Medicine Department of Neuroscience is parent organization of: Mouse Mutagenesis Center for Developmental Defects is parent organization of: Gene Atlas is parent organization of: Dictyostelium discoideum genome database is parent organization of: Bovine Genome Project is parent organization of: BCM ET is parent organization of: Atlas2 is parent organization of: Genboree Workbench is parent organization of: BCM Analyte Center is parent organization of: BCM Circulating Tumor Cells Core Facility is parent organization of: Baylor College of Medicine Human Genome Sequencing Center is parent organization of: Mouse Genome Project is parent organization of: Dictyostelium discoideum genome database |
ISNI:0000 0001 2111 2894, Crossref funder ID:100007492, nlx_50627, grid.252890.4, Wikidata:Q812573 | https://ror.org/005781934 | SCR_011029 | 2026-08-01 12:04:19 | 1 | ||||||||||
|
ABySS-Explorer Resource Report Resource Website 1+ mentions |
ABySS-Explorer (RRID:SCR_010980) | ABySS-Explorer | software resource | An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. | is listed by: OMICtools | OMICS_00873 | SCR_010980 | 2026-08-01 12:04:18 | 3 |
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