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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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caArray Resource Report Resource Website 10+ mentions |
caArray (RRID:SCR_006053) | caArray | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management. | microarray, gene expression, data sharing, service resource, data management, annotation, interoperability, life sciences |
is listed by: re3data.org is listed by: OMICtools is related to: Cancer Biomedical Informatics Grid is related to: MAGE-TAB has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151452, OMICS_00864, r3d100010573 | https://doi.org/10.17616/R33G76 | SCR_006053 | SciCrunch Registry | caArray - Array Data Management System, caArray Data Portal | 2026-11-07 11:56:10 | 35 | |||||
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MetaQC Resource Report Resource Website 10+ mentions |
MetaQC (RRID:SCR_006000) | software resource | Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision. | standalone software, mac os x, unix/linux, windows, r, FASEB list |
is listed by: OMICtools has parent organization: CRAN |
PMID:22116060 | GNU General Public License, v2 | OMICS_04032 | https://github.com/donkang34/MetaQC | SCR_006000 | SciCrunch Registry | MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis, MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis | 2026-11-07 11:55:47 | 40 | ||||||
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DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | data or information resource, data repository, database, service resource, storage service resource | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; Scientific Research Fund of Heilongjiang Provincial Education Department ; State Key Laboratory of Urban Water Resource and Environment |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth, https://bio.tools/diseasemeth | http://202.97.205.78/diseasemeth/ | SCR_005942 | SciCrunch Registry | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2026-11-07 11:55:43 | 44 | ||||
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BLESS Resource Report Resource Website 10+ mentions |
BLESS (RRID:SCR_005963) | BLESS | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory. | c++, next-generation sequencing, bloom-filter, error correction, ngs, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24451628 | GNU General Public License v3 | OMICS_02246, biotools:bless | https://bio.tools/bless | SCR_005963 | SciCrunch Registry | BLoom-filter-based Error correction Solution for high-throughput Sequencing reads, BLESS - Bloom-filter-based Error Correction Tool for NGS reads | 2026-11-07 11:55:46 | 46 | |||||
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OMPdb Resource Report Resource Website |
OMPdb (RRID:SCR_006221) | OMPdb | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | beta-barrel, outer membrane protein, gram-negative bacteria, protein, protein sequence, transmembrane, annotation, genome-wide analyses, comparative genomics, sequence, structure, blast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20952406 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01611, biotools:ompdb, nlx_151768 | https://bio.tools/ompdb | SCR_006221 | SciCrunch Registry | OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria | 2026-11-07 11:56:11 | 0 | |||||
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deepSNV Resource Report Resource Website 10+ mentions |
deepSNV (RRID:SCR_006214) | deepSNV | software resource | Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants). | data import, genetic variability, genetics, snp, sequencing, single nucleotide variant, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24443148 | GNU General Public License, v3 | OMICS_02239, biotools:deepsnv | https://bio.tools/deepsnv | SCR_006214 | SciCrunch Registry | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-11-07 11:55:50 | 34 | |||||
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PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | data processing software, software application, software resource, source code | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip, https://sources.debian.org/src/phylip/ | SCR_006244 | SciCrunch Registry | PHYLogeny Inference Package | 2026-11-07 11:56:06 | 3544 | |||||
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pepStat Resource Report Resource Website 1+ mentions |
pepStat (RRID:SCR_006240) | software resource | Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization. | standalone software | is listed by: OMICtools | PMID:23770318 | OMICS_04027 | SCR_006240 | SciCrunch Registry | 2026-11-07 11:55:51 | 8 | |||||||||
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ScerTF Resource Report Resource Website 10+ mentions |
ScerTF (RRID:SCR_006121) | ScerTF | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Catalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region. | binding site, transcription factor, regulatory site, gene, regulation, regulatory interaction, matrix, nucleotide sequence, dna sequence, yeast, position weight matrix, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIGMS R01 GM078222; NHGRI HG00249 |
PMID:22140105 | biotools:scertf, nlx_151599, OMICS_00542 | http://ural.wustl.edu/ScerTF, https://bio.tools/scertf | http://ural.wustl.edu/TFDB/ | SCR_006121 | SciCrunch Registry | 2026-11-07 11:56:05 | 19 | |||||
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estMOI Resource Report Resource Website 10+ mentions |
estMOI (RRID:SCR_006192) | estMOI | software resource | A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt). | multiplicity of infection, parasite, genome, high throughput sequencing, single nucleotide polymorphism, chromosome | is listed by: OMICtools | PMID:24443379 | Free, Public | OMICS_02240 | SCR_006192 | SciCrunch Registry | estMOI - Estimating multiplicity of infection using parasite deep sequencing data | 2026-11-07 11:56:11 | 10 | ||||||
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PhyloBayes Resource Report Resource Website 100+ mentions |
PhyloBayes (RRID:SCR_006402) | PhyloBayes | software resource | A Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenomic, multigene alignment, alignment, reconstruction |
is listed by: OMICtools has parent organization: University of Montreal; Quebec; Canada |
PMID:24318999 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02212 | SCR_006402 | SciCrunch Registry | PhyloBayes - phylogenetic reconstruction using infinite mixtures | 2026-11-07 11:55:54 | 486 | ||||||
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KOBAS Resource Report Resource Website 5000+ mentions |
KOBAS (RRID:SCR_006350) | KOBAS | analysis service resource, data analysis service, production service resource, service resource, software resource | Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ortholog, pathway, disease, gene, protein, annotation, command line, FASEB list |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: OMIM is related to: Pathway Interaction Database is related to: BioCarta Pathways is related to: Reactome is related to: BioCyc is related to: PANTHER is related to: FunDO is related to: Genetic Association Database is related to: GWAS: Catalog of Published Genome-Wide Association Studies has parent organization: Peking University; Beijing; China |
PMID:21715386 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02228 | SCR_006350 | SciCrunch Registry | KEGG Orthology Based Annotation System | 2026-11-07 11:56:12 | 5008 | ||||||
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SNPdryad Resource Report Resource Website 1+ mentions |
SNPdryad (RRID:SCR_006414) | SNPdryad | service resource | Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences. | non-synonymous, single nucleotide polymorphism, ortholog, protein sequence |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:24389653 | OMICS_02198 | SCR_006414 | SciCrunch Registry | SNPdryad - Deleterious Non-Synonymous SNP Predictions for Human | 2026-11-07 11:55:52 | 3 | |||||||
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QCGWAS Resource Report Resource Website 1+ mentions |
QCGWAS (RRID:SCR_006408) | QCGWAS | software resource | Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies. | quality control, genome wide association study, windows, os x, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24395754 | GNU General Public License, v3 or later | OMICS_02203, biotools:qcgwas | https://bio.tools/qcgwas | SCR_006408 | SciCrunch Registry | QCGWAS: Quality Control of Genome Wide Association Study results, Quality Control of Genome Wide Association Study | 2026-11-07 11:55:54 | 7 | |||||
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PredictSNP Resource Report Resource Website 100+ mentions |
PredictSNP (RRID:SCR_006327) | PredictSNP | analysis service resource, data analysis service, production service resource, service resource, software resource | Consensus classifier tool that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database. A stand-alone version is also available. | single nucleotide polymorphism, classifier, prediction, mutation, protein function, FASEB list |
is listed by: OMICtools is related to: Protein Mutant Database is related to: UniProt |
PMID:24453961 | Free for academic use | OMICS_02218 | SCR_006327 | SciCrunch Registry | PredictSNP - Consensus classifier for prediction of disease-related mutations | 2026-11-07 11:56:07 | 148 | ||||||
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OMIM Resource Report Resource Website 5000+ mentions |
OMIM (RRID:SCR_006437) | OMIM, MIM | catalog, data or information resource, database | Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources. | gene, genetics, phenotype, genotype, genetic loci, mutation, clinical, trait, disorder, umls, ontology, gold standard, FASEB list |
is used by: Human Phenotype Ontology is used by: NIF Data Federation is used by: MitoMiner is used by: Schizo-Pi is used by: GEMINI is used by: MARRVEL is used by: HmtPhenome is listed by: BioPortal is listed by: OMICtools is related to: HomoloGene is related to: TopoSNP is related to: phenomeNET is related to: Integrated Gene-Disease Interaction is related to: OMIA - Online Mendelian Inheritance in Animals is related to: Europhenome Mouse Phenotyping Resource is related to: Homophila is related to: Biomine is related to: MalaCards is related to: PhenoTips is related to: KOBAS is related to: Integrated Manually Extracted Annotation is related to: aGEM is related to: biomaRt has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA has parent organization: NCBI works with: Human Mouse Disease Connection works with: Database of genes related to Repeat Expansion Diseases |
Genetic disorder, Mendelian disorder, Developmental disorder | PMID:22477700 PMID:22470145 PMID:21472891 PMID:19728286 PMID:18842627 PMID:18428346 PMID:17642958 PMID:17357067 PMID:15608251 PMID:15360913 PMID:11752252 PMID:10845565 PMID:10612823 PMID:9805561 PMID:7937048 PMID:1867277 |
Restricted | nif-0000-03216, r3d100010416, OMICS_00278 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim, http://www.ncbi.nlm.nih.gov/Omim/, http://purl.bioontology.org/ontology/OMIM, https://doi.org/10.17616/R3188W | SCR_006437 | SciCrunch Registry | Online Mendelian Inheritance in Man, OMIM - Online Mendelian Inheritance in Man, MIM, The Online Mendelian Inheritance in Man Morbid Map | 2026-11-07 11:56:13 | 7365 | ||||
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GeneCommittee Resource Report Resource Website |
GeneCommittee (RRID:SCR_004168) | geneCommittee | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. | dna, microarray, rna-seq, gene expression, classification, gene set, gene, gene set enrichment, functional annotation |
is listed by: OMICtools has parent organization: University of Vigo; Galicia; Spain |
PMID:24475928 | Acknowledgement requested | OMICS_02291 | https://github.com/michada/GeneCommittee | SCR_004168 | SciCrunch Registry | 2026-11-07 11:55:45 | 0 | ||||||
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Babel Resource Report Resource Website 100+ mentions |
Babel (RRID:SCR_004307) | Babel | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | windows, macos x |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01530 | SCR_004307 | SciCrunch Registry | babel: Ribosome profiling data analysis | 2026-11-07 11:55:19 | 175 | |||||||
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PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm, https://sources.debian.org/src/perm/ | SCR_004223 | SciCrunch Registry | PERiodic seed Mapping, Periodic seed Mapping | 2026-11-07 11:55:45 | 60 | ||||||
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EGAPP Resource Report Resource Website 1+ mentions |
EGAPP (RRID:SCR_004189) | EGAPP | data or information resource, portal, topical portal | Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team. | genetic test, genomics, clinical, genomic technology, evaluation, public health |
is listed by: OMICtools has parent organization: Centers for Disease Control and Prevention |
OMICS_01538 | SCR_004189 | SciCrunch Registry | Evaluation of Genomic Applications in Practice and Prevention (EGAPP), Evaluation of Genomic Applications in Practice and Prevention | 2026-11-07 11:55:18 | 1 |
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