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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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QUAST Resource Report Resource Website 1000+ mentions |
QUAST (RRID:SCR_001228) | QUAST | software resource | Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots. | genome assembly, genomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia has parent organization: SourceForge |
PMID:23422339 | biotools:quast, OMICS_02115 | https://bio.tools/quast, https://sources.debian.org/src/quast/ | SCR_001228 | SciCrunch Registry | QUAST: Quality Assessment Tool for Genome Assemblies | 2026-09-26 02:12:56 | 3293 | ||||||
|
R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | SciCrunch Registry | 2026-09-26 02:12:55 | 4 | ||||||||
|
Academy Biomedical Company Resource Report Resource Website |
Academy Biomedical Company (RRID:SCR_001108) | commercial organization | Commercial antibody supply company that focuses on providing antibodies for research in cardiovascular and atherosclerosis. | antibody, cardiovascular, athersclerosis, antibody supplier | nlx_152249 | SCR_001108 | SciCrunch Registry | Academy Bio-Medical Company, Academy Biomedical Company Inc. | 2026-09-26 02:12:55 | 0 | ||||||||||
|
TileQC Resource Report Resource Website |
TileQC (RRID:SCR_001229) | TileQC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh). | next-generation sequencing, quality control, solexa, r, tile, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Oregon State University; Oregon; USA |
PMID:18507856 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tileqc, OMICS_02114 | https://bio.tools/tileqc | SCR_001229 | SciCrunch Registry | TileQC: A tile based approached to quality control | 2026-09-26 02:12:56 | 0 | |||||
|
ChanTest Resource Report Resource Website 10+ mentions |
ChanTest (RRID:SCR_001220) | CT | commercial organization | An ion channel focused Contract Research Organization (CRO) that does safety testing and screening for global pharma and biotech companies. ChanTest has developed a complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers. Services range from early functional screens for profiling drug candidates or ranking within profiles during the drug-discovery process to a complete set of in vitro GLP service products for cardiac risk assessment. ChanTest works in partnership with customers to speed the drug-development process, save time and money, and ultimately to help make better, safer drugs. | ion channel, safety testing, screening, drug, drug development | nlx_152331 | http://chantest.com | SCR_001220 | SciCrunch Registry | ChanTest.com | 2026-09-26 02:12:56 | 12 | ||||||||
|
BreakFusion Resource Report Resource Website 1+ mentions |
BreakFusion (RRID:SCR_001102) | BreakFusion | software resource | Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data. | computational pipeline, gene fusions, rna, sequence, data, perl, c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:22563071 DOI:10.1093/bioinformatics/bts272 |
Free, Available for download, Freely available | OMICS_01342 | SCR_001102 | SciCrunch Registry | 2026-09-26 02:12:55 | 3 | |||||||
|
Body System Terms from ICD11 Resource Report Resource Website |
Body System Terms from ICD11 (RRID:SCR_001252) | ICD11-BODYSYSTEM | controlled vocabulary, data or information resource, ontology | Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision | owl | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157339 | SCR_001252 | SciCrunch Registry | 2026-09-26 02:12:57 | 0 | ||||||||
|
RCASPAR Resource Report Resource Website |
RCASPAR (RRID:SCR_001253) | RCASPAR | software resource | Software package for survival time prediction based on a piecewise baseline hazard Cox regression model. It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. | gene expression, genetics, proteomics, visualization, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02087 | SCR_001253 | SciCrunch Registry | 2026-09-26 02:12:57 | 0 | ||||||||
|
CNVtools Resource Report Resource Website 10+ mentions |
CNVtools (RRID:SCR_001250) | CNVtools | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies. | genetic variability, copy number variant, genetic association |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18776912 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02090 | SCR_001250 | SciCrunch Registry | CNVtools - A package to test genetic association with CNV data | 2026-09-26 02:12:57 | 12 | ||||||
|
CGEN Resource Report Resource Website 10+ mentions |
CGEN (RRID:SCR_001251) | CGEN | data analysis software, data processing software, software application, software resource | Software R package for analysis of case-control studies in genetic epidemiology. | genetic, epidemiology, r, case-control, clustering, multiple comparison, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21387464 | Free, Available for download, Freely available | OMICS_02089 | SCR_001251 | SciCrunch Registry | CGEN - An R package for analysis of case-control studies in genetic epidemiology | 2026-09-26 02:12:57 | 18 | ||||||
|
NPEBseq Resource Report Resource Website 1+ mentions |
NPEBseq (RRID:SCR_001014) | NPEBseq | software resource | A method for non-parametric, empirical Bayesian-based analysis of RNA-seq count data. | rna, rna sequence, seq, empirical, Bayesian, nonparametric | is listed by: OMICtools | PMID:23981227 | OMICS_01312 | http://bioinformatics.wistar.upenn.edu/NPEBseq | SCR_001014 | SciCrunch Registry | 2026-09-26 02:12:54 | 1 | |||||||
|
SABER Resource Report Resource Website 50+ mentions |
SABER (RRID:SCR_001257) | SABER | software resource | Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels. | r, linux, ancestry, admixed, genetic, population, linkage disequilibrium, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University School of Medicine; California; USA |
PMID:16773560 | Free, Available for download, Freely available | biotools:saber, OMICS_02081 | https://bio.tools/saber | SCR_001257 | SciCrunch Registry | 2026-09-26 02:12:57 | 72 | ||||||
|
SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | SciCrunch Registry | 2026-09-26 02:12:53 | 1 | ||||||
|
Hytest Resource Report Resource Website 1+ mentions |
Hytest (RRID:SCR_001133) | commercial organization | A commercial antibody supplier that specializes in high-quality monoclonal antibodies and antigens for the diagnostic industry. | antibody, monoclonal, antigen, diagnostic, research and development, r and d | nlx_152378, grid.417767.4, Wikidata: Q5952196 | https://ror.org/031cpdm45 | SCR_001133 | SciCrunch Registry | HyTest Ltd. | 2026-09-26 02:12:55 | 5 | |||||||||
|
ASC Resource Report Resource Website 1+ mentions |
ASC (RRID:SCR_001013) | ASC | software resource | Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available. | sample variation, rna, dna, biology, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brown University; Rhode Island; USA |
biotools:sqn, OMICS_01298 | https://bio.tools/sqn | SCR_001013 | SciCrunch Registry | 2026-09-26 02:12:54 | 1 | ||||||||
|
BioLegend Resource Report Resource Website 5000+ mentions |
BioLegend (RRID:SCR_001134) | commercial organization | Commercial antibody supplier and developer for biomedical research. These products are compatible with use in flow cytometry and mass cytometry, immunoprecipitation and chip, western blotting, immunofluorescence microscopy, and quantitative multiplexing. | commercial, antibody, reagent, biomedical, research, san diego | nlx_152302 | SCR_001134 | SciCrunch Registry | 2026-09-26 02:12:55 | 6621 | |||||||||||
|
multtest Resource Report Resource Website 10+ mentions |
multtest (RRID:SCR_001255) | multtest | software resource | Software package for non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. | differential expression, microarray, multiple comparison, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:multtest, OMICS_02085 | https://bio.tools/multtest | SCR_001255 | SciCrunch Registry | multtest - Resampling-based multiple hypothesis testing | 2026-09-26 02:12:57 | 37 | ||||||
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GDC Resource Report Resource Website 1+ mentions |
GDC (RRID:SCR_001007) | GDC | data analysis software, data management software, data processing software, software application, software resource | A C++ application designed for compression of genome collections from the same species. | compression, genome collection, c++, genome, software |
is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/srep11565 | Source code available for download | OMICS_00958 | https://github.com/refresh-bio/GDC2 | SCR_001007 | SciCrunch Registry | GDC 2, Genome Differential Compressor, Genome Differential Compressor (GDC) | 2026-09-26 02:12:53 | 1 | |||||
|
NewEast Biosciences Resource Report Resource Website |
NewEast Biosciences (RRID:SCR_001129) | commercial organization | Commercial supplier which provides antibodies, assay kits, biomarkers, and proteins. | antibody, pennsylvania, commercial, assay kit, oncogene | nlx_152421 | SCR_001129 | SciCrunch Registry | 2026-09-26 02:12:55 | 0 | |||||||||||
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Mutation Surveyor Resource Report Resource Website 500+ mentions |
Mutation Surveyor (RRID:SCR_001247) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects. | dna, sequencing, dna-seq, sanger sequencing, sequence analysis software | is listed by: OMICtools | PMID:21780000 PMID:20938837 |
Restricted | OMICS_01816 | Mutation Surveyor software version 5.0 | http://www.softgenetics.com/mutationSurveyor.html | SCR_001247 | SciCrunch Registry | 2026-09-26 02:12:56 | 668 |
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