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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pyrocleaner Resource Report Resource Website 1+ mentions |
Pyrocleaner (RRID:SCR_000584) | Pyrocleaner | software resource | A software module for cleaning 454 pyrosequencing reads using filters such as read duplication, length, complexity, base-pair quality and number of undetermined bases. The software also uses flowgram files of paired-end sequences to validate paired-ends files of another file. | pyrosequence, assembly, rna, dna, duplication, length, complexity, bases, flowgram, paired end | is listed by: OMICtools | PMID:21615897 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01069 | SCR_000584 | 2026-07-25 12:04:48 | 1 | |||||||
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GeneExpressionSignature Resource Report Resource Website 1+ mentions |
GeneExpressionSignature (RRID:SCR_000455) | software resource | An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest. | software package, r, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23374109 | Free, Available for download, Freely available | OMICS_04919 | SCR_000455 | GeneExpressionSignature - Gene Expression Signature based Similarity Metric | 2026-07-25 12:04:46 | 1 | |||||||
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flowQ Resource Report Resource Website |
flowQ (RRID:SCR_000575) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05805 | SCR_000575 | flowQ: Quality control for flow cytometry | 2026-07-25 12:04:48 | 0 | ||||||||
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SigFuge Resource Report Resource Website |
SigFuge (RRID:SCR_000444) | software resource | Algorithm for testing significance of clustering in RNA-seq data. | software package, unix/linux, mac os x, windows, r, clustering, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25030904 | Free, Available for download, Freely available | OMICS_05201 | SCR_000444 | 2026-07-25 12:04:46 | 0 | ||||||||
|
VariantMaster Resource Report Resource Website |
VariantMaster (RRID:SCR_000569) | VariantMaster | software resource | Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores. | unix/linux, clinical, genetics, high throughput sequencing, monogenic disease, variant, snp, indel |
is listed by: OMICtools has parent organization: SourceForge |
Genetic disease, Tumor | PMID:24389049 | Free, Available for download, Freely available, | OMICS_02261 | SCR_000569 | VariantMaster - Extract causative variants for monogenic and sporadic genetic diseases | 2026-07-25 12:04:48 | 0 | |||||
|
CorQ Resource Report Resource Website 1+ mentions |
CorQ (RRID:SCR_000660) | software resource | A set of perl programs that correct errors in 454 pyrosequences by identifying and flagging poor quality insertions, deletions and substitutions within an alignment. The algorithm utilizes the inherent base quality in sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors. | homopolymer, indel, corq, uneven read mapping, pyrosequence error, forward errors |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
PMID:24039850 | OMICS_01039 | SCR_000660 | 2026-07-25 12:04:50 | 1 | |||||||||
|
DeNovoGear Resource Report Resource Website 1+ mentions |
DeNovoGear (RRID:SCR_000670) | software resource | A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations. | de novo, mutation, sequence, dna, rna, error modeling, exome analysis |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:23975140 | Free, Available for download, Freely available | OMICS_00083 | https://github.com/denovogear/denovogear | SCR_000670 | 2026-07-25 12:04:48 | 3 | |||||||
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SRMA Resource Report Resource Website |
SRMA (RRID:SCR_000669) | SRMA | software resource | A post-alignment micro re-aligner for next-generation high throughput sequencing data. | matlab, sequence re-alignment, command-line, java, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20932289 | Free, Available for download, Freely available | biotools:srma, OMICS_01079 | https://bio.tools/srma | SCR_000669 | Short Read Micro re-Aligner | 2026-07-25 12:04:50 | 0 | |||||
|
KLEIO Resource Report Resource Website 1+ mentions |
KLEIO (RRID:SCR_000698) | KLEIO | service resource | An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008 | semantic search, entity recognition |
is listed by: FORCE11 is listed by: OMICtools is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | Acknowledgement required, See Terms of Use | OMICS_01186, nlx_44954 | http://www.nactem.ac.uk/software/kleio/ | SCR_000698 | 2026-07-25 12:04:50 | 3 | ||||||
|
FineSplice Resource Report Resource Website 1+ mentions |
FineSplice (RRID:SCR_000691) | software resource | A software pipeline based on TopHat2 combined with a splice junction detection algorithm. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24574529 | Free, Available for download, Freely available | OMICS_03274 | SCR_000691 | 2026-07-25 12:04:48 | 1 | ||||||||
|
jmzIdentML API Resource Report Resource Website |
jmzIdentML API (RRID:SCR_000878) | software resource | A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. | standalone software, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:22539429 | Free, Available for download, Freely available | OMICS_03339 | SCR_000878 | 2026-07-25 12:04:51 | 0 | ||||||||
|
SciRoKo Resource Report Resource Website 1+ mentions |
SciRoKo (RRID:SCR_000941) | software resource | Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output. | genomics, comparative, genome, microsatellite, analysis, investigation | is listed by: OMICtools | PMID:17463017 | Free, Available for download, Freely available | OMICS_00113 | SCR_000941 | 2026-07-25 12:04:51 | 6 | ||||||||
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EMI Resource Report Resource Website |
EMI (RRID:SCR_001171) | EMI | software resource | Clustering software which uses pairwise identity-by-descent (IBD) segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and extends clusters across sliding windows in the genome. | clustering, identity-by-descent |
is listed by: OMICtools has parent organization: Aarhus University; Aarhus; Denmark |
PMID:24363374 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02186 | SCR_001171 | Efficient Multiple-IBD | 2026-07-25 12:04:56 | 0 | ||||||
|
Shimmer Resource Report Resource Website |
Shimmer (RRID:SCR_001164) | software resource | Software package that detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. It uses Fisher's exact test along with multiple testing correction (Benjamini-Hochberg) to find significant differences between allele composition with a specified false discovery rate. | standalone software, bam |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
PMID:23620360 | Free, Available for download, Freely available | OMICS_03612 | SCR_001164 | 2026-07-25 12:04:55 | 0 | ||||||||
|
DiMO Resource Report Resource Website 1+ mentions |
DiMO (RRID:SCR_001168) | DiMO | software resource | Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. | r, motif, perceptron |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:24369152 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02190 | SCR_001168 | Discriminative Motif Optimizer, DiMO: Discriminative Motif Optimizer | 2026-07-25 12:04:56 | 1 | ||||||
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ExomePeak Resource Report Resource Website 1+ mentions |
ExomePeak (RRID:SCR_001076) | exomePeak | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. | r, matlab |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Texas at San Antonio; Texas; USA |
PMID:23589649 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00570 | SCR_001076 | 2026-07-25 12:04:55 | 4 | |||||||
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ParticleCall Resource Report Resource Website |
ParticleCall (RRID:SCR_001103) | ParticleCall | software resource | A base-calling algorithm for Illumina DNA sequencing. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22776067 | OMICS_01154 | SCR_001103 | 2026-07-25 12:04:55 | 0 | ||||||||
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Google Compute Engine Resource Report Resource Website 1+ mentions |
Google Compute Engine (RRID:SCR_001011) | Compute Engine | service resource | An infrastructure as a service that lets you run your large-scale computing workloads on Linux virtual machines hosted on Google's infrastructure. | cloud | is listed by: OMICtools | OMICS_01204 | SCR_001011 | 2026-07-25 12:04:53 | 2 | |||||||||
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CUDA-EC Resource Report Resource Website 1+ mentions |
CUDA-EC (RRID:SCR_001090) | CUDA-EC | software resource | A fast parallel error correction tool for short reads. | c, gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20426693 | Free, Available for download, Freely available | OMICS_01100, biotools:cuda-ec | https://bio.tools/cuda-ec | SCR_001090 | Compute Unified Device Architecture | 2026-07-25 12:04:54 | 1 | |||||
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qips Resource Report Resource Website |
qips (RRID:SCR_001092) | qips | software resource | A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase. | command-line, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_00457 | SCR_001092 | 2026-07-25 12:04:56 | 0 |
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