For sharing scripts on analyses of MedulloBlastoma patient-derived xenograft (MB-PDX) of Visium spatial RNA-seq between Palbociclib treated & control samples.
Used Python 3.7.10. Python dependency install:
pip install -r requirements.txt
Need to install stLearn and add to your python path:
git clone https://github.com/BiomedicalMachineLearning/stLearn.git
For R scripts, see session info in docs/r_session.md
docs/ -> Contains project documentation.
index.md -> Index which describes each script in scripts/ in terms of
INPUT/OUTPUT, and brief description of function.
r_session.md -> Details on the r session used to run the R scripts.
figure_components/ -> Contains the outputted components which are used to
create the paper figures. Is grouped according to
the figure. You can see index.md for which script
generates what figure components by checking the
script OUTPUT description.
scripts/ -> Contains the scripts described in docs/index.md.
Scripts are grouped into folders relating to order & analysis
performed.
X1_QC_SpeciesClassify/ -> Contains scripts related to spot QC &
classifying spots by human/mouse/mix.
X2_DEAnalysis/ -> Contains scripts related to the DE analysis between
Palbo treated & control samples pseudobulked by
human/mix/mouse spots.
Also includes PCA & GSEA analyses.
X3_GiottoEnrichment/ -> Contains scripts related to the Giotto
enrichment analysis ('Per-spot enrichment').
X4_HumanSpotAnnotation/ -> Contains scripts related to annotating
human spots
by dominant cell type using reference
scRNA-seq data using SingleR.
X5_MouseSpotAnnotation/ -> Contains scripts related to annotating
mouse spots
by dominant cell type using reference
scRNA-seq data using SingleR.
X6_CellCellInteraction/ -> Contains code related to called ligand-
receptor & cell-cell interactions in the
interface region for human & mouse tissue.
X7_revision-analysis/ -> Analysis conducted during revision process,
performed by Dr. Guiyan Ni, and Onkar Mulay.