Transcript level data frame from Example dataset for spatial transcriptional profiling of tissue

The example dataset is based on one run of SMI RNA readout for FFPE melanoma tissue samples. It contains information for 1375 cells with 756783 transcripts within a cropped region of one single FOV of 1 tissue section.

Usage

data(mini_transcriptDF)

Format

An object of class "data.frame" with 756783 transcripts in row and 9 variables

UMI_transID

unique id for transcript

UMI_cellID

unique id for cell based on original cell segmentaion assignment

x

spatial coordinate of the transcript in x-axis of the given FOV, unit in micron

y

spatial coordinate of the transcript in y-axis of the given FOV, unit in micron

z

spatial coordinate of the transcript in z-axis of the given FOV, unit in micron

target

gene identity of given transcript

slide

slide ID of given transcript

fov

fov ID of given transcript

CellId

the cell label assignment of given transcript within given FOV based on original cell segmentation

See also

ori_CellStatsDF for corresponding cell level dataset, ori_RawExprs for corresponding cell x gene expression matrix