Software

scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling
Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) and single-cell RNA sequencing (scRNA-seq) provide a …
Qile Yang, Ksenia R. Safina, Kieu Diem Quynh Nguyen, Zewen Kelvin Tuong, Nick Borcherding
PDF Code DOI Pubmed
scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling
dandelionR: Single-cell immune repertoire trajectory analysis in R
Integration of single-cell RNA-sequencing (scRNA-seq) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) is extremely powerful …
Jiawei Yu, Xiaohan Xu, Nick Borcherding, Zewen Kelvin Tuong
PDF DOI Pubmed
bHIVE
B-cell Hybrid Immune Virtual Evolution model for artificial immune system simulation
Code
dandelionR
Single-cell immune repertoire trajectory analysis in R
Code
immReferent
Reference interface to IMGT and OGRDB for immune receptor and HLA sequences
Code
immApex
Tools for adaptive immune receptor sequence-based machine and deep learning
Code
Ibex
Autoencoder for single-cell BCR
PDF Code
Ibex
scRepertoire v2
A toolkit for single-cell immune profiling
Code
scRepertoire v2
Trex
Autoencoder for single-cell TCR
Code
Trex
Mapping the immune environment in clear cell renal carcinoma by single-cell genomics
Clear cell renal cell carcinoma (ccRCC) is one of the most immunologically distinct tumor types due to high response rate to …
Nick Borcherding, Ajaykumar Vishwakarma, Andrew P. Voigt, Andrew Bellizzi, Jacob Kaplan, Kenneth Nepple, Aliasger K Salem, Russell W Jenkins, Yousef Zakharia, Weizhou Zhang
PDF Code DOI Pubmed
Mapping the immune environment in clear cell renal carcinoma by single-cell genomics