You will find bash and R scripts in two distincts directories.
-
xenomeCreation.sh
create the genome reference based on 10X tutorial that will be used by Cell Ranger. -
align10x.sh
run Cell Ranger alignment for the several samples. -
filterMouseReads.sh
remove reads that mapped on mouse and create clean fasta with reads specific to human. -
qualityControl.R
make plots to check quality. -
filterCells.R
filter single cells (based on previous generated figures) Seurat Object and save it to Clean.rds file on disk. Thresholds are stored in files containted in the data directory. -
DE-speudoBulk.R
retrieve individual Clean.rds files from previous step and do speudo-bulk differential expression analysis between two conditions. -
clusterCells.R
from the rds object containing filtered seurat object for each condition , you apply seurat normalisation and save in an _integrated.rds file... ( can be 2 or several conditions) -
plotclusterCells.R
load the integrated.rds file.. -
scfGSEA.R
fSGEA for speudo-bulk RnaSeq. -
tsne.R
plot tsne or umap for several experiments.
In bash/triggers
, there is bash scripts that call (trigger) other bash scripts...
-
trigger_filterMouseReads.sh
call filterMouseReads.sh for several samples. -
trigger_main.sh
calls sequentially bash scripts in core directory that call the core main R scriptsqualityControl.R
,filterCells.R
,DE-speudoBulk.R
andscfGSEA.R
for several samples/conditions.
Mix of R and pythons stuffs.
-
veloctyo.sh
: You create loom files using dir from 10x samples using velocyto. -
plotNestedCluster.R
: tsne.R adaptatation. Will combined samples, run Umap Tsnse (need to extract list of genes differentially expressed per cluster) save files to disk to be reused by python scripts latter. -
loom_combine.py
: combine several loom files. (loom file are generated from dispached 10x samples per experiment) -
velocyto.R
: Read the loom, transform to seurat, RunPCA, applied all seurat stuffs...and finaly run RunVelocity -
velocyto2.R
: Read the loom and finally save h5ad file that can be use as starting point for velocyto.py. -
velocyto.py
: start from h5ad file and plot trajectories , velocity related plots.