This repository contains all the needed code and metadata files to analyze and generate figures for Huang L. et al. Nature 2024
In order to set up a running environment, run the provided preprocessing.ipynb script.
Other scripts should run in this order:
figure1.ipynb
figure2.ipynb
figure3.ipynb
Please send questions to Amir Giladi: a.giladi@hubrecht.eu
Package versions:
plotrix 3.7-6
plyr 1.8.7
reshape2 1.4.4
Hmisc 4.4-1
Formula 1.2-4
survival 3.2-11
lattice 0.20-41
flowWorkspace 3.34.0
flowCore 1.52.0
ggrepel 0.9.1
ggplot2 3.3.3
org.Hs.eg.db 3.10.0
AnnotationDbi 1.48.0
Biobase 2.46.0
ChIPpeakAnno 3.20.0
VennDiagram 1.6.20
futile.logger 1.4.3
GenomicRanges 1.38.0
GenomeInfoDb 1.22.0
Biostrings 2.54.0
XVector 0.26.0
IRanges 2.20.0
S4Vectors 0.24.0
BiocGenerics 0.32.0
clusterProfiler 3.14.0
RColorBrewer 1.1-3
metacell 0.3.5
SeuratDisk 0.0.0.9019