# A Framework for visualizing gene set enrichment throughout neurodevelopment

## Documentation for package ‘brainImageR’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

available_areanames | List of areas that are present in a plotted brain slice
BrainMap | Internal- Overlaps regional enrichment into a single section
brainrange | brainrange
Comp | Comp keeps track of Spatial Enrichment calculations and parameters
Comp-class | Comp keeps track of Spatial Enrichment calculations and parameters
CreateBrain | Overlap spatial enrichment information and anatomical organization
dat | In vitro temporal data of human neural progenitor cells and neurons
GetGenes | GenGenes
hipp | Hippocampal genes using the adult human brain as reference
InABA | Quick search for presence of genes in the ABA list
PlotBrain | Color and Plot the SGSE image
PlotEnrich | PlotEnrich
PlotPred | Plot your temporal predictions
Pred | Pred
Pred-class | Pred
predict_time | Predict developmental time from gene expression data
PValue.onetail | Calculate p-value from bootstrapped sample
RandomTissueSummary | Generate a random overlap
reColor | Color in the brain images based on enrichment values
SpatialEnrichment | Calculate the presence of your gene set within each brain region
testEnrich | Calculate significance of gene set enrichment
TissueSummary | Internal-Identify the number of genes expressed in each tissue
tis_in_region | List of regions that are supported by given tissue
tis_set | List of tissues that support a given region in the brain plot
vth | VTH genes identified from Allen Brain Atlas developing human
whichtissues | Identify the tissues where a set of genes are expressed