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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NGSadmix Resource Report Resource Website 100+ mentions |
NGSadmix (RRID:SCR_003208) | NGSadmix | software resource | A tool for finding admixture proportions from next generation sequencing (NGS) data that is based on genotype likelihoods. It is a multithreaded c/c++ program. | next generation sequencing, admixture proportion, admixture, genotype, c, c++, admixture, association study, population structure, resequencing |
is listed by: OMICtools has parent organization: University of Copenhagen; Copenhagen; Denmark |
PMID:24026093 | Acknowledgement requested | OMICS_01553 | SCR_003208 | SciCrunch Registry | 2026-10-24 12:44:53 | 144 | |||||||
|
PHAST Resource Report Resource Website 50+ mentions |
PHAST (RRID:SCR_003204) | PHAST | software resource | A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code. | evolutionary genomic, evolution, genomics, sequence alignment, phylogenetic tree, genomic annotation, functional element, protein-coding exon, conserved sequence, phylogenetic modeling, ancestral sequence, c |
is listed by: OMICtools is listed by: Debian has parent organization: Cornell University; New York; USA |
NIH ; David and Lucile Packard Foundation ; NHGRI ; University of California Biotechnology Research and Education Program ; NSF DBI-0644111; NIGMS R01-GM082901-01 |
PMID:21278375 DOI:10.1093/bib/bbq072 |
Free, Available for download, Freely available | OMICS_01557 | https://sources.debian.org/src/phast/ | SCR_003204 | SciCrunch Registry | Phylogenetic Analysis with Space/Time Models | 2026-10-24 12:44:57 | 69 | ||||
|
miR-PREFeR Resource Report Resource Website 1+ mentions |
miR-PREFeR (RRID:SCR_003353) | software resource | An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24930140 | Free, Available for download, Freely available | biotools:mir-prefer, OMICS_04637 | https://bio.tools/mir-prefer | SCR_003353 | SciCrunch Registry | miRNA PREdiction From small RNA-Seq data, miR-PREFeR: microRNA PREdiction From small RNAseq data | 2026-10-24 12:44:56 | 8 | ||||||
|
PicTar Resource Report Resource Website 1000+ mentions |
PicTar (RRID:SCR_003343) | PicTar | software resource | An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets | microrna target, microrna, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
PMID:15806104 | Free, Available for download, Freely available | OMICS_00411, biotools:pictar, nif-0000-31983 | http://pictar.mdc-berlin.de/, https://bio.tools/pictar | SCR_003343 | SciCrunch Registry | 2026-10-24 12:44:58 | 1717 | ||||||
|
BlockClust Resource Report Resource Website 1+ mentions |
BlockClust (RRID:SCR_003347) | software resource | Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. | is listed by: OMICtools | PMID:24931994 | Free, Available for download, Freely available | OMICS_04641 | SCR_003347 | SciCrunch Registry | 2026-10-24 12:44:56 | 1 | |||||||||
|
EasyqpcR Resource Report Resource Website 1+ mentions |
EasyqpcR (RRID:SCR_003406) | EasyqpcR | data analysis software, data processing software, software application, software resource | Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. | qpcr, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02313 | https://www.bioconductor.org/packages//2.13/bioc/html/EasyqpcR.html | SCR_003406 | SciCrunch Registry | 2026-10-24 12:44:57 | 9 | |||||||
|
NanoStriDE Resource Report Resource Website 10+ mentions |
NanoStriDE (RRID:SCR_003407) | NanoStriDE | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Web application that accepts the raw count data produced by the NanoString nCounter analysis system, normalizes it according to guidelines provided by NanoString Technologies, performs differential expression analysis on the normalized data, and provides a heatmap of the results from the differential expression analysis. | normalization, differential expression, nanostring ncounter, heatmap |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:22177214 | Free, Freely available | OMICS_02307 | SCR_003407 | SciCrunch Registry | NanoStriDE - NanoString Differential Expression, NanoString Differential Expression | 2026-10-24 12:44:57 | 11 | ||||||
|
PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; China NSFC ; NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | SciCrunch Registry | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-10-24 12:44:56 | 1441 | |||
|
GEOSS Resource Report Resource Website 1+ mentions |
GEOSS (RRID:SCR_003401) | GEOSS | software resource | A complete software system used to store and analyze gene expression data. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Virginia; Virginia; USA |
Free, Freely available | OMICS_00764 | SCR_003401 | SciCrunch Registry | Gene Expression Open Source System, GEOSS - Gene Expression Open Source System, GEOSS Gene Expression Open Source System, GeneX Va | 2026-10-24 12:44:57 | 1 | ||||||||
|
NormqPCR Resource Report Resource Website 50+ mentions |
NormqPCR (RRID:SCR_003388) | NormqPCR | software resource | Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data. | gene expression, microtitre plate assay, qpcr, reference gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22748112 | Free, Available for download, Freely available | OMICS_02315, biotools:normqpcr | https://bio.tools/normqpcr | SCR_003388 | SciCrunch Registry | NormqPCR - Functions for normalisation of RT-qPCR data | 2026-10-24 12:44:56 | 55 | |||||
|
BestKeeper Resource Report Resource Website 1000+ mentions |
BestKeeper (RRID:SCR_003380) | BestKeeper | software resource | Excel-based tool using pair-wise correlations for determination of stable housekeeping genes, differentially regulated target genes and sample integrity. It determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points. | gene, excel, quantification, rt-qpcr, gene expression, target gene, differential expression |
is used by: RefFinder is listed by: OMICtools has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:15127793 | Free, Available for download, Freely available | OMICS_02318 | http://bestkeeper.gene-quantification.info/ | http://www.wzw.tum.de/gene-quantification/bestkeeper.html | SCR_003380 | SciCrunch Registry | 2026-10-24 12:44:56 | 1188 | |||||
|
Amplicon Resource Report Resource Website 1000+ mentions |
Amplicon (RRID:SCR_003294) | Amplicon | software resource | Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac | python, pcr primer, pcr, primer, tkinter, windows, dna sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:14962918 | Free, Available for download, Freely available | OMICS_02329 | http://www.aad.gov.au/amplicon | SCR_003294 | SciCrunch Registry | 2026-10-24 12:44:58 | 1955 | ||||||
|
Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | data or information resource, data repository, database, image repository, service resource, storage service resource | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD P41 HD064556; NICHD R01 HD045776 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | SciCrunch Registry | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-10-24 12:44:54 | 484 | ||||
|
Spanki Resource Report Resource Website 1+ mentions |
Spanki (RRID:SCR_004469) | Spanki | software resource | A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data. | windows | is listed by: OMICtools | PMID:24209455 | OMICS_01414 | SCR_004469 | SciCrunch Registry | Splicing Analysis Kit | 2026-10-24 12:45:12 | 8 | |||||||
|
PASHA Resource Report Resource Website 10+ mentions |
PASHA (RRID:SCR_004455) | PASHA | software resource | A parallel short read assembler for large genomes using de Bruijn graphs. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21867511 | OMICS_00024 | SCR_004455 | SciCrunch Registry | 2026-10-24 12:45:12 | 10 | |||||||||
|
miRDeepFinder Resource Report Resource Website 1+ mentions |
miRDeepFinder (RRID:SCR_004456) | miRDeepFinder | software resource | Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing. | is listed by: OMICtools | PMID:22290409 | OMICS_00362 | SCR_004456 | SciCrunch Registry | 2026-10-24 12:45:12 | 2 | |||||||||
|
Kdetrees Resource Report Resource Website |
Kdetrees (RRID:SCR_004522) | software resource | R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. | applet, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24764459 | GNU General Public License, v2 | biotools:kdetrees, OMICS_04172 | https://github.com/grady/kdetrees, https://bio.tools/kdetrees | SCR_004522 | SciCrunch Registry | kdetrees: Nonparametric method for identifying discordant phylogenetic trees | 2026-10-24 12:45:13 | 0 | ||||||
|
VIROME Resource Report Resource Website 10+ mentions |
VIROME (RRID:SCR_004362) | VIROME | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | open-reading frame, metagenome, virus, environment, sequence, library, genetic, polymorphism, orfan, environmental sequencing, shotgun metagenomics, viral ecology, function, taxonomy, peptide, blast |
is listed by: OMICtools is related to: UniRef is related to: CAMERA is related to: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis has parent organization: University of Delaware; Delaware; USA has parent organization: University of Maryland School of Medicine; Maryland; USA |
Gordon and Betty Moore Foundation ; NSF award 0959894 |
PMID:23407591 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01506 | SCR_004362 | SciCrunch Registry | Viral Informatics Resource for Metagenome Exploration, Viral Informatics Resource for Metagenome Exploration - VIROME | 2026-10-24 12:45:11 | 22 | |||||
|
VAMPS Resource Report Resource Website 10+ mentions |
VAMPS (RRID:SCR_004483) | VAMPS | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally. |
is listed by: OMICtools has parent organization: Marine Biological Laboratory |
Alfred P. Sloan Foundation ; NSF ; NASA Astrobiology Institute |
PMID:24499292 | Public, The community can contribute to this resource | OMICS_01501 | SCR_004483 | SciCrunch Registry | VAMPS Project, Visualization and Analysis of Microbial Population Structure | 2026-10-24 12:45:12 | 28 | ||||||
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SnoopCGH Resource Report Resource Website 1+ mentions |
SnoopCGH (RRID:SCR_004420) | SnoopCGH | software resource | A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:19687029 | biotools:snoopcgh, OMICS_00736 | https://bio.tools/snoopcgh | SCR_004420 | SciCrunch Registry | 2026-10-24 12:45:11 | 2 |
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