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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-08-08 11:59:25 | 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 | 2026-08-08 11:59:40 | 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 | 2026-08-08 11:59:40 | 250 | ||||||||||
|
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 | 2026-08-08 11:59:25 | 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 | 2026-08-08 11:59:38 | 31 | ||||||||
|
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 | 2026-08-08 11:59:38 | 1 | |||||||||
|
BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | sequence analysis software, image analysis software, software resource, software application, data analysis software, alignment software, data processing software | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/, https://bio.tools/bwa-sw, https://sources.debian.org/src/bwa/ | SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-08-08 11:59:39 | 2638 | |||||
|
CloudBurst Resource Report Resource Website |
CloudBurst (RRID:SCR_010911) | CloudBurst | software resource | A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19357099 | Free | OMICS_00657, biotools:cloudburst | https://bio.tools/cloudburst | SCR_010911 | 2026-08-08 11:59:25 | 0 | ||||||
|
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 | 2026-08-08 11:59:40 | 48 | ||||||||||
|
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 | 2026-08-08 11:59:39 | 84 | ||||||||||
|
HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-08-08 11:59:38 | 5929 | |||||
|
Carleton University; Ontario; Canada Resource Report Resource Website |
Carleton University; Ontario; Canada (RRID:SCR_011136) | university | Public comprehensive university in Ottawa, Ontario, Canada. Founded in 1942 as Carleton College, a private, non-denominational evening college to serve returning World War II. |
is parent organization of: Aptamer Base is parent organization of: An Extended and Parallel version of Clustal is parent organization of: Carleton University Tissue Engineering and Applied Materials Hub Core Facility |
Crossref funder ID:100008095, grid.34428.39, Wikidata:Q1041737, nlx_45745, ISNI:0000 0004 1936 893X | https://ror.org/02qtvee93 | SCR_011136 | 2026-08-08 11:59:43 | 0 | ||||||||||
|
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 | 2026-08-08 11:59:42 | 46 | |||||||||
|
Medical Research Council Resource Report Resource Website 50+ 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 | 2026-08-08 11:59:41 | 55 | ||||||||
|
Catholic University of Louvain; Louvain-la-Neuve; Belgium Resource Report Resource Website 1+ mentions |
Catholic University of Louvain; Louvain-la-Neuve; Belgium (RRID:SCR_011141) | UCL | university | Belgium's largest French speaking university. |
is related to: Pharma-Planta Consortium is related to: PRECISESADS is parent organization of: Catholic University of Louvain Institute of Experimental and Clinical Research Imaging Platform Core Facility is parent organization of: Catholic University of Louvain Institute of Experimental and Clinical Research Flow Cytomerty Platform Core Facility is parent organization of: Catholic University of Louvain Genomics platform Core Facility |
grid.7942.8, Wikidata:Q378134, ISNI:0000 0001 2294 713X, nlx_143960, Crossref funder ID:501100008135 | https://ror.org/02495e989 | http://www.uclouvain.be/en-index.html | SCR_011141 | Catholic University of Louvain, Universit� catholique de Louvain, Universite catholique de Louvain | 2026-08-08 11:59:45 | 2 | |||||||
|
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 | 2026-08-08 11:59:42 | 12 | ||||||||
|
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 | 2026-08-08 11:59:43 | 37 | |||||||||
|
Center for Information Technology Resource Report Resource Website |
Center for Information Technology (RRID:SCR_011143) | CIT | government granting agency | The Center for Information Technology''s (CIT) mission is to provide, coordinate, and manage information technology and to advance computational science. CIT incorporates the power of modern computers into the biomedical programs and administrative procedures of the NIH by focusing on three primary activities: conducting computational biosciences research, developing computer systems, and providing computer facilities. CIT supports NIH''s research and management programs with efficient, cost-effective administrative and high-powered scientific computing, software development, networking, and telecommunications services. CIT also provides bioinformatics support through its scientists, engineers, and mathematicians. Among its activities, the CIT: * engages in collaborative research and provides collaborative support to NIH investigators in the area of computational bioscience * provides efficient, cost-effective information systems and networking services * provides state-of-the-art scientific and administrative computing facilities * identifies new computing technologies with innovative applications to biomedical research * creates, purchases, and distributes software applications * provides NIH staff with computing information, expertise, and training * provides data-processing and high-performance computing facilities, integrated telecommunications data networks, and services to the U.S. Department of Health and Human Service (HHS) and other Federal agencies * serves as a data center to HHS and other Federal agencies * develops, administers, and manages NIH systems and provides consulting services to NIH Institutes and Centers in support of administrative and business applications |
has parent organization: National Institutes of Health is parent organization of: Federal Interagency Traumatic Brain Injury Research Informatics System is parent organization of: MIPAV: Medical Image Processing and Visualization |
nlx_inv_1005031 | SCR_011143 | 2026-08-08 11:59:27 | 0 | ||||||||||
|
Central University of the Caribbean; Puerto Rico; USA Resource Report Resource Website |
Central University of the Caribbean; Puerto Rico; USA (RRID:SCR_011145) | UCC | university | Private university in Bayamón, Puerto Rico that focuses on graduate studies and professional certifications in the health sciences. |
is parent organization of: UCC Common Instrumentation Area and Services is parent organization of: UCC Behavioral Testing Facility is parent organization of: UCC Biomedical Proteomic Facility is parent organization of: UCC Data Management and Statistical Research Support Unit is parent organization of: UCC HIV and Substance of Abuse Laboratory Core is parent organization of: UCC Immunocytochemistry Laboratory is parent organization of: UCC Neuronal Glia Culture Facility is parent organization of: UCC Optical Imaging Facility is parent organization of: UCC Protein and Nucleic Acid Core Facility is parent organization of: UCC Transmission Electron Microscopy Laboratory |
grid.253922.d, Wikidata:Q5061968, nlx_156113, ISNI:0000 0000 9699 6324 | https://ror.org/01rpmzy83 | SCR_011145 | Universidad Central del Caribe, Central University of the Caribbean | 2026-08-08 11:59:43 | 0 | ||||||||
|
UNC Microarray Database Resource Report Resource Website 10+ mentions |
UNC Microarray Database (RRID:SCR_010979) | UNC MD, UNCMD | data or information resource, database, service resource, storage service resource, data repository | Database for microarray data storage, retrieval, analysis, and visualization. | microarray, FASEB list |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Account required, The community can contribute to this resource | OMICS_00872 | SCR_010979 | UNC-Chapel Hill Microarray Database | 2026-08-08 11:59:26 | 33 |
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