Punkst Modules

Punkst provides several command-line tools for analyzing high resolution spatial (transcriptomics) data. Each module can be used individually or as part of a pipeline.

Available Modules

• pts2tiles: Groups pixels to tiles for faster processing
• tiles2hex: Groups pixels into non-overlapping hexagons for spot level analysis
• lda4hex: Runs LDA on the spot level data
• pixel-decode: Annotates each pixel with the top factors and their probabilities
• Visualization: Visualizes the pixel level analysis results

Input Data Format

The input is a tsv file with the following columns: X, Y, feature, count. Whether the file contains headers or other columns is not relevant, as long as the above four columns are present.

• X, Y coordinates can be either integer or float vlaues. (If your coordinates are integers and you would like to keep the original coordinates in the pixel level inference output, set --coords-are-int in punkst pixel-decode). The coordinates can be in arbitrary units, just make sure all scale/size related parameters you later provide should be in the same unit.

• "feature" can be a string or a nonnegative integer corresponding to the index in a feature list.

• "count" is a nonnegative integer. You could apply gene-specific non-negative real valued weights to the count later in analysis.