Easily Downloads a Gene Expression Dataset from a GEO Code and
Retrieves the Gene Symbols of Its Probesets
A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293,  GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.

Gene Haplotype Statistics, Phenotype Association and
Visualization
Import genome variants data and perform gene haplotype Statistics,
visualization and phenotype association with 'R'.
c(person(given = "Zhang",
family = "Renliang",
email = "zhang_renliang@163.com",
role = c("aut", "cre")),
person(given = "Jia",
family = "Guanqing",
email = "jiaguanqing@caas.cn",
role = c("aut")))
ape, Biostrings, ggpubr, GenomicRanges, magrittr, maps,
methods, muscle, IRanges, pegas, reshape2, rlang, rtracklayer,
trackViewer, stats, stringdist, stringr, tibble, tidyr, utils,
vcfR
Zhang Renliang [aut, cre],
Jia Guanqing [aut]

A Pipeline to Define Gene Families in Legumes and Beyond
c(
person("Jose V.", "Die", email = "jose.die@uco.es", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7506-8590")),
person("Moamen M.", "Elmassry", email = "moamen.elmassry@ttu.edu", role = c("aut")),
person("Kimberly H.", "LeBlanc", email = "kimberly.leblanc@nih.gov", role = c("aut")),
person("Olaitan I.", "Awe", email = "laitanawe@gmail.com", role = c("aut")),
person("Allissa","Dillman", email = "Allissa.Dillman@nih.gov", role = c("aut")),
person("Ben", "Busby", email = "Ben.Busby@nih.gov", role = c("aut")))
A pipeline with high specificity and sensitivity in extracting
proteins from the RefSeq database (National Center for Biotechnology
Information). Manual identification of gene families is highly
time-consuming and laborious, requiring an iterative process of manual and
computational analysis to identify members of a given family. The pipelines
implements an automatic approach for the identification of gene families
based on the conserved domains that specifically define that family. See
Die et al. (2017) <doi:10.1101/436659> for more information and examples.
Jose V. Die [aut, cre] (<https://orcid.org/0000-0002-7506-8590>),
Moamen M. Elmassry [aut],
Kimberly H. LeBlanc [aut],
Olaitan I. Awe [aut],
Allissa Dillman [aut],
Ben Busby [aut]