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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SeqSite Resource Report Resource Website |
SeqSite (RRID:SCR_013243) | SeqSite | software resource | Software for detecting transcription factor binding sites from ChIP-seq data. | is listed by: OMICtools | OMICS_00493 | SCR_013243 | SeqSite: ChIP-Seq Binding Site Identification | 2026-08-01 12:04:47 | 0 | |||||||||
|
Repitools Resource Report Resource Website 10+ mentions |
Repitools (RRID:SCR_013242) | Repitools | software resource | Software tools for the analysis of enrichment-based epigenomic data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00619 | SCR_013242 | 2026-08-01 12:04:57 | 21 | ||||||||||
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PIAGE Resource Report Resource Website |
PIAGE (RRID:SCR_013124) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program that performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman''s (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154534, SCR_009372, nlx_154594 | SCR_013124 | R/PIAGE, Power of Indirect Association Studies of Gene-Environment Interactions | 2026-08-01 12:04:55 | 0 | ||||||||
|
SmashCommunity Resource Report Resource Website 1+ mentions |
SmashCommunity (RRID:SCR_013245) | SmashCommunity | software resource | A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. |
is listed by: OMICtools has parent organization: EMBL - Bork Group |
OMICS_01482 | SCR_013245 | 2026-08-01 12:04:46 | 8 | ||||||||||
|
Entrez Utilities Resource Report Resource Website 10+ mentions |
Entrez Utilities (RRID:SCR_013249) | software resource |
Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment. Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course. User Requirements: Please read for important information on scripting NCBI servers. EInfo: Provides field index term counts, last update, and available links for each database. ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment. EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies. ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment. EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment. ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs. EGQuery: Provides Entrez database counts in XML for a single search using Global Query. ESpell: Retrieves spelling suggestions. SOAP Interface for Entrez Utilities PMID to PMC ID Converter Entrez DTDs Demonstration Program Announcement Mailing List Leasing Data from the National Library of Medicine Help Desk User Requirements Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following: Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests. Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address. Make no more than 3 requests every 1 second. Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem. NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel. |
has parent organization: National Library of Medicine | nif-0000-30519 | http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html | SCR_013249 | Entrez Utilities | 2026-08-01 12:04:47 | 21 | |||||||||
|
BrainVisa Morphology extensions Resource Report Resource Website 1+ mentions |
BrainVisa Morphology extensions (RRID:SCR_013248) | BrainVisa Morphology extensions | software resource | An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa | analyze, c++, image display, linux, macos, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, shape analysis, software, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVISA / Anatomist is related to: INCF Software Center |
Artistic License | nlx_155716 | http://www.nitrc.org/projects/brainvisa_ext | SCR_013248 | 2026-08-01 12:04:57 | 1 | |||||||
|
miRSeqNovel Resource Report Resource Website 1+ mentions |
miRSeqNovel (RRID:SCR_013257) | miRSeqNovel | software resource | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
Free, Public, Non-commercial | OMICS_00381 | SCR_013257 | 2026-08-01 12:04:46 | 2 | |||||||||
|
AutoMap Resource Report Resource Website 50+ mentions |
AutoMap (RRID:SCR_013095) | AutoMap | software resource | A tool for structural biology and drug design. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01596 | SCR_013095 | 2026-08-01 12:04:45 | 92 | ||||||||||
|
DynamicProg Resource Report Resource Website |
DynamicProg (RRID:SCR_013217) | DynamicProg | software resource | A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01150 | SCR_013217 | 2026-08-01 12:04:57 | 0 | ||||||||||
|
A Catalogue of Illusions Resource Report Resource Website |
A Catalogue of Illusions (RRID:SCR_013186) | image collection, data or information resource | Set of different illusions, including color illusions, motion illusions, and optic illusions. Most illusions are from Professor Akiyoshi Kitaoka of the Ritsumeikan University in Kyoto, Japan. | color, illusion, motion, optical, vision | has parent organization: Ritsumeikan University; Kyoto; Japan | nif-0000-24679 | SCR_013186 | Catalogue of Illusions | 2026-08-01 12:04:56 | 0 | |||||||||
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muliAlignFree Resource Report Resource Website |
muliAlignFree (RRID:SCR_013188) | muliAlignFree | software resource | R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
PMID:23990418 | Free | OMICS_00981 | SCR_013188 | muliAlignFree: Multiple Alignment-free Sequence Comparison | 2026-08-01 12:04:46 | 0 | |||||||
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U.S. Public Health Service Commissioned Corps Resource Report Resource Website 1+ mentions |
U.S. Public Health Service Commissioned Corps (RRID:SCR_013104) | USPHS | institution | Commissioned Corps of the United States Public Health Service, is the federal uniformed service of the U.S. Public Health Service, and is one of the eight uniformed services of the United States. | Government granting agency | nlx_152565, Crossref funder ID: 100007197, ISNI: 0000 0001 1554 5300, grid.417684.8, Wikidata: Q476322 | https://ror.org/05xf94514 | SCR_013104 | US Public Health Service Commissioned Corps, U.S. Public Health Service | 2026-08-01 12:04:55 | 7 | ||||||||
|
National Institute for Occupational Safety and Health Resource Report Resource Website |
National Institute for Occupational Safety and Health (RRID:SCR_013180) | NIOSH, OH | institution | http://www.cdc.gov/niosh/oep/funding.html |
has parent organization: Centers for Disease Control and Prevention is parent organization of: Adult Blood Lead Epidemiology and Surveillance Interactive Database |
nlx_inv_1005099, grid.416809.2, ISNI: 0000 0004 0423 0663, Wikidata: Q60346, Crossref funder ID: 100000125 | https://ror.org/0502a2655 | SCR_013180 | 2026-08-01 12:04:45 | 0 | |||||||||
|
CancerMutationAnalysis Resource Report Resource Website |
CancerMutationAnalysis (RRID:SCR_013181) | CancerMutationAnalysis | software resource | Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer. |
is listed by: OMICtools has parent organization: Bioconductor |
Cancer | OMICS_00141 | SCR_013181 | 2026-08-01 12:04:46 | 0 | |||||||||
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-08-01 12:04:47 | 37 | ||||||
|
LifeScope Resource Report Resource Website 100+ mentions |
LifeScope (RRID:SCR_013234) | LifeScope | software resource | Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC). | unix/linux, life technologies, linux, next-generation sequencing | has parent organization: Life Technologies | Acknowledgement requested | OMICS_00667 | SCR_013234 | LifeScope Genomic Analysis Software | 2026-08-01 12:04:57 | 199 | |||||||
|
CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | 2026-08-01 12:04:56 | 1 | ||||||||||
|
CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-08-01 12:04:46 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-08-01 12:04:56 | 66 | ||||||||||
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HMMSplicer Resource Report Resource Website 1+ mentions |
HMMSplicer (RRID:SCR_013315) | HMMSplicer | software resource | An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
OMICS_01241 | SCR_013315 | 2026-08-01 12:04:47 | 3 |
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