PDAC analysis scripts

Scripts for PDAC Stereo-seq and scRNA-seq data analysis.

Requirements

Note: The scripts in the repository have only been tested in a Linux system.

Software	Version	Website
Python	3.9.13	https://www.python.org/
R	4.1.1	https://www.r-project.org/
STAR	2.7.1a	https://github.com/alexdobin/STAR
PISA	0.7-24	https://github.com/shiquan/PISA
StereoCell	1.0.6	https://github.com/BGIResearch/StereoCell
Seurat	3.1.2	https://satijalab.org/seurat/
RcppML	0.5.6	https://github.com/zdebruine/RcppML
cNMF	1.4.1	https://github.com/dylkot/cNMF
inferCNV	1.12.0	https://github.com/broadinstitute/infercnv
SAW	5.1.3	https://github.com/STOmics/SAW
Stereopy	0.13.0b1	https://github.com/STOmics/Stereopy
SPACEL	1.1.6	https://github.com/QuKunLab/SPACEL
scvi-tools	0.20.3	https://github.com/scverse/scvi-tools
Scanpy	1.10.0	https://github.com/scverse/scanpy
pySCENIC	0.12.1	https://github.com/aertslab/pySCENIC
Metascape	3.5	https://metascape.org/
Squidpy	1.2.3	https://github.com/scverse/squidpy
Monocle 2	2.22.0	http://cole-trapnell-lab.github.io/monocle-release
CellChat	1.6.1	https://github.com/sqjin/CellChat
NicheNetR	2.0.2	https://github.com/saeyslab/nichenetr
Cytoscape	3.9.1	https://cytoscape.org/
NetworkX	2.8.7	https://networkx.org/
Scipy	1.11.1	https://github.com/scipy/scipy
harmony	0.0.9	https://github.com/slowkow/harmonypy
ClusterGVis	0.1.1	https://github.com/junjunlab/ClusterGVis