Correspinding to Figures 1, 2.

NMFproj is available here https://github.com/yyoshiaki/NMFprojection.

Reference mapping by symphony is available here https://github.com/yyoshiaki/screfmapping. The code needed for each project is included in the directory. Additionally, meta_analysis.v2.R is the analysis for the meta-analysis. Summary stats are availble here doi : 10.6084/m9.figshare.23983038.

Pipeline are available in another repository https://github.com/yyoshiaki/sclinker-skg.

Single-cell data can be explored interactively and downloaded in SingleCellPortal https://singlecell.broadinstitute.org/single_cell/study/SCP1963.

Single-cell transcriptome landscape of circulating CD4+ T cell populations in human autoimmune diseases Yoshiaki Yasumizu, Daiki Takeuchi, Reo Morimoto, Yusuke Takeshima, Tatsusada Okuno, Makoto Kinoshita, Takayoshi Morita, Yasuhiro Kato, Min Wang, Daisuke Motooka, Daisuke Okuzaki, Yamami Nakamura, Norihisa Mikami, Masaya Arai, Xuan Zhang, Atsushi Kumanogoh, Hideki Mochizuki, Naganari Ohkura, Shimon Sakaguchi bioRxiv 2023.05.09.540089; doi: https://doi.org/10.1101/2023.05.09.540089