Package 'geisha'

GEISHA Expression Data (expression.txt)

Description

This dataset contains NCBI Gene ID, NCBI Gene Name, GEISHA ID, Ensembl ID, GO terms, embryo stages and tissue locations.

Usage

expression_txt

Format

A tibble of 7 variables (columns):

ncbi_gene_id

NCBI gene identifier.

ensembl_gene_id

Ensembl gene identifier.

gene_name

NCBI gene name.

stages

Hamilton-Hamburger stages.

locations

Anatomical location.

geisha_id

GEISHA identifier.

gene_ontology_id

Gene ontology identifier.

Data set generation workflow can be found at the source of this package in data-raw/data.R.

Source

Original dataset from: http://geisha.arizona.edu/geisha/expression.txt.

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GEISHA Expression Data (expression.xml)

Description

This dataset contains NCBI Gene ID, NCBI Gene Name, GEISHA ID, embryo stages and tissue locations.

Usage

expression_xml

Format

A tibble of 5 variables (columns):

ncbi_gene_id

NCBI gene identifier.

gene_name

NCBI gene name.

geisha_id

GEISHA identifier.

stage

Hamilton-Hamburger stages.

location

Anatomical location.

Data set generation workflow can be found at the source of this package in data-raw/data.R.

Source

Original dataset from: http://geisha.arizona.edu/geisha/expression.xml.

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Get dates of last update of download files

Description

This function will scrape on-the-fly GEISHA's downloads page and retrieve the date of last update of the to-be-downloaded files.

Usage

get_dates_of_last_update(files = download_files())

Arguments

files

file names to whose update date is to be checked in the downloads page.

Value

Returns a tibble with one file per row.

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Get the files available to download from GEISHA

Description

This function retrieves those files available for download from the downloads' page of the GEISHA website. These files are saved to data-raw/ are meant to be used only by the package developer.

Usage

get_files(files = download_files())

Arguments

files

The name of the files to be downloaded. This parameter is set by default to download all available files.

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Hamilton-Hamburguer stages

Description

This function returns a character vector of Hamilton-Hamburguer (HH) stages.

Usage

hh_stages(hh_prefix = FALSE)

Arguments

hh_prefix

A logical indicating whether to include the prefix 'HH' in the after-laying egg stages, i.e., those stages numbered with arabic numerals.

Value

A character vector of Hamilton-Hamburguer (HH) stages.

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Date of last update of download files

Description

Date of last update of download files

Usage

last_updates

Format

A tibble of 2 variables:

file

File name.

date

Date of last update by GEISHA.

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Imports data-raw/expression.txt as a tibble

Description

This function reads data-raw/expression.txt as a tibble. This function is meant to be used only by the developer of this package.

Usage

read_expression_txt()

Value

Returns a tibble with the data present in expression.txt.

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Imports data-raw/expression.xml as a tibble

Description

This function reads data-raw/expression.xml as a tibble. This function is meant to be used only by the developer of this package.

Usage

read_expression_xml()

Value

Returns a tibble with (part of) the data present in expression.xml.

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