This repository contains the code used in our single cell sequencing paper: "Follicular T Cells are Clonally and Transcriptionally Distinct in B Cell-Driven Autoimmune Disease"
https://www.nature.com/articles/s41467-021-27035-8
No installation necessary
Model data is included in the data directory.
- Download
dataandcodedirectories - Set
dataas the working directory - Download
gexandvdjdata from GSE157649, available here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157649 - Run each script in numerical order in either Rstudio or Python. These scripts will generate the figures presented in our manuscript.
NB: Expected total run time is 3-5 days
CellRanger 10X Genomics v4.0.0
R The Comprehensive R Archive Network v3.6.1
Rstudio v1.2.1578
2017PWM https://bitbucket.org/slofgren/antigen-id-paper-code/src/master/ N/A
GLIPH2 http://50.255.35.37:8080/ v2
scanpy https://pypi.org/project/scanpy/ v1.5.1
vegan https://cran.r-project.org/web/packages/vegan/ v2.5-6
qgraph https://cran.r-project.org/web/packages/qgraph v1.6.5
immunarch https://immunarch.com/ v0.5.5
ggseqlogo https://omarwagih.github.io/ggseqlogo/ v0.1
msigdbr https://cran.r-project.org/web/packages/msigdbr v7.0.1
clusterProfiler https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html v3.14.3
pheatmap https://cran.r-project.org/web/packages/pheatmap/ v1.0.12
vennDiagram https://cran.r-project.org/web/packages/VennDiagram v1.6.20
ggpubr https://rpkgs.datanovia.com/ggpubr/ v0.2.5.999
EnhancedVolcano https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html v1.4.0
biomaRt https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html v2.42.0
ggplot2 https://ggplot2.tidyverse.org/ v3.3.0
Seurat https://satijalab.org/seurat/ v3.1.4
anndata2ri https://github.com/theislab/anndata2ri v1.0.2
DEseq2 https://bioconductor.org/packages/release/bioc/html/DESeq2.html v1.26.0
DeepTCR https://github.com/sidhomj/DeepTCR v1.4.15