Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Reverse TCR repertoire evolution toward dominant low-affinity clones during chronic CMV infection

(2020) Kilian Schober et al.   NATURE IMMUNOLOGY

T‐cell receptor immunosequencing reveals altered repertoire diversity and disease‐associated clonal expansions in ankylosing spondylitis patients

(2020) Aimee L. Hanson et al.   Arthritis & Rheumatology

Dual TCR T Cells: Identity Crisis or Multitaskers?

(2019) Nathaniel J. Schuldt et al.   JOURNAL OF IMMUNOLOGY

Next-generation computational tools for interrogating cancer immunity

(2019) Francesca Finotello et al.   NATURE REVIEWS GENETICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

AIRR Community Standardized Representations for Annotated Immune Repertoires

(2018) Jason Anthony Vander Heiden et al.   Frontiers in Immunology

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

(2016) Jeff Daily   BMC BIOINFORMATICS

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS