Results 11 to 20 of about 7,703,039 (197)
clusterProfiler: an R package for comparing biological themes among gene clusters.
Omics, 2012 Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment ...
Guangchuang Yu +3 more
semanticscholar +1 more source
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Nucleic Acids Res., 2012 SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary ...
Christian Quast +7 more
semanticscholar +1 more source
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Nature Biotechnology, 2013 Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities.
M. Langille +11 more
semanticscholar +1 more source
GSVA: gene set variation analysis for microarray and RNA-Seq data
BMC Bioinformatics, 2013 Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary.
Sonja Hänzelmann +2 more
semanticscholar +1 more source
Integrating diverse genomic data using gene sets
Genome Biology, 2011 We introduce and evaluate data analysis methods to interpret simultaneous measurement of multiple genomic features made on the same biological samples. Our tools use gene sets to provide an interpretable common scale for diverse genomic information.
Svitlana Tyekucheva +3 more
semanticscholar +1 more source
ShinyGO: a graphical gene-set enrichment tool for animals and plants
Bioinform., 2019 MOTIVATION Gene lists are routinely produced from various genome-wide studies. Enrichment analysis can link these gene lists with underlying molecular pathways and functional categories such as gene ontology (GO) and other databases.
S. X. Ge, Dongmin Jung, Runan Yao
semanticscholar +1 more source
Genome Biology, 2013 TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat.
Daehwan Kim +5 more
semanticscholar +1 more source
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
BMC Bioinformatics, 2013 System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge.
Edward Y. Chen +7 more
semanticscholar +1 more source
Population Ecology, Volume 67, Issue 2, Page 109-124, April 2025.In the process of captive breeding and reintroduction of endangered animal species, it is crucial to minimize familial bias in reproductive success during the reintroduction phase to preserve genetic diversity. In this study, we attempted to identify the familial lineage of individuals of the endangered bagrid fish Tachysurus ichikawai born at the ...
Hinano Mizuno +5 more
wiley +1 more source
Argonaute—a database for gene regulation by mammalian microRNAs
BMC Bioinformatics, 2005 BackgroundThe Sulston score is a well-established, though approximate metric for probabilistically evaluating postulated clone overlaps in DNA fingerprint mapping.
Priyanka Shahi +9 more
semanticscholar +1 more source