In ramiromagno/geisha: GEISHA Expression Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
library(geisha)

geisha

{geisha} is an R data package that provides the expression dataset from the Gallus Expression in Situ Hybridization Analysis (GEISHA) project.

The data here provided is of r last_updates$date[1]. You can check whether this is the latest version by visiting http://geisha.arizona.edu/geisha/downloads.jsp.

Installation

You can install the current version of geisha with:

# install.packages("remotes")
remotes::install_github("ramiromagno/geisha")

Usage

At this moment this package provides only two datasets: expression_txt and expression_xml.

Dataset `expression_txt`

library(geisha)

expression_txt

Each row refers to a gene found to be expressed in the chick embryo at a specific set of Hamilton-Hamburger stages (stages) and anatomical locations (locations), obtained from a specific source (indicated by the geisha_id).

Please note that the columns stages and locations are list-columns.

Dataset `expression_xml`

Contrary to expression_txt that only lists the stages and the locations when/where a gene is found expressed, in the object expression_xml you can actually know the relationship between stage and location, i.e., which stages associate with which locations.