In ndhutso/geneSummary: Summarize GEOquery data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(geneSummary)

Shiny

A shiny app that allows for data to be imported from the NCBI GEO database. Different data tables can be generated and saved.

Extract expression matrix (extExp)

This function extracts the numerical gene expression data. It is in BioConductor format with genes as rows and samples as columns.

Extract sample matrix (extSample)

This function extracts the annotations for each sample. This is information about each sample such as sample characteristics and cell type.

Extract gene annotation (extGene)

This function extracts the annotations for each gene. This is information about the measurement of each gene such as sequencing of the gene and probe ID.

Filter data tables (filterTbl)

This function filters data tables by values in each of their columns. If the table is of the type "Gene Expression", then simple numeric filters with inputs such as "<10" can be used on the sample columns. Other filters require exact value inputs.

ndhutso/geneSummary documentation built on Nov. 4, 2019, 8:43 p.m.