code and data you can use
Tools & data
Software from the lab and its collaborators, and the datasets we have released with Scientific Data.
Software
GENTLE
Generates features and builds classifiers from T cell repertoire cancer data. Runs as a web app or locally in Python.
PathSingle
Pathway activity scores for single-cell data that place T cells in their cell states.
YADA
Reference-free deconvolution of bulk RNA sequencing data into cell-type proportions.
PathWeigh
Pathway activity scores from RNA-seq, following the behavior of biochemical pathway cascades.
AIRR-ML 2025 solution
Predicts disease state from immune repertoires across eight datasets, matching a model to each dataset.
Datasets
Pre-treatment TCR repertoires in colorectal cancer
Data access is described in the paper's data availability statement.
TCR repertoires in ovarian cancer and healthy donors
Data access is described in the paper's data availability statement.
Murine TCR repertoires over time after immunotherapy
Data access is described in the paper's data availability statement.
Transcriptome of the medicinal leech central nervous system
Data access is described in the paper's data availability statement.