The DAVIDQuery package in Bioconductor: Retrieving data from the DAVID Bioinformatics Resource
نویسندگان
چکیده
DAVID (Database for Annotation, Visualization and Integrated Discovery) is a bioinformatics resource developed by the National Institute of Allergy and Infectious Diseases at Frederick in conjunction with the Laboratory of Immunopathogenesis and Bioinformatics (LIB), SAIC Frederick. This resource is described as “a graph theory evidence-based method to agglomerate speciesspecific gene/protein identifiers the most popular resources including NCBI, PIR and Uniprot/SwissProt. It groups tens of millions of identifiers into 1.5 million unique protein/gene records.” Further information can be found in published articles [1][2].
منابع مشابه
girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
UNLABELLED The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals. Moreover, the package operates within and extends the ever-growing Bioconductor framework ...
متن کاملeasyRNASeq: a bioconductor package for processing RNA-Seq data
MOTIVATION RNA sequencing is becoming a standard for expression profiling experiments and many tools have been developed in the past few years to analyze RNA-Seq data. Numerous 'Bioconductor' packages are available for next-generation sequencing data loading in R, e.g. ShortRead and Rsamtools as well as to perform differential gene expression analyses, e.g. DESeq and edgeR. However, the process...
متن کاملinSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO
Microarray technology has become an integral part of biomedical research and increasing amounts of datasets become available through public repositories. However, re-use of these datasets is severely hindered by unstructured, missing or incorrect biological samples information; as well as the wide variety of preprocessing methods in use. The inSilicoDb R/Bioconductor package is a command-line f...
متن کاملpsygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes
Motivation Psychiatric disorders have a great impact on morbidity and mortality. Genotype-phenotype resources for psychiatric diseases are key to enable the translation of research findings to a better care of patients. PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts. Results We present psygenet2r, an R package t...
متن کاملHiTC: exploration of high-throughput 'C' experiments
SUMMARY The R/Bioconductor package HiTC facilitates the exploration of high-throughput 3C-based data. It allows users to import and export 'C' data, to transform, normalize, annotate and visualize interaction maps. The package operates within the Bioconductor framework and thus offers new opportunities for future development in this field. AVAILABILITY AND IMPLEMENTATION The R package HiTC is...
متن کامل