11. Session info¶
The versions this tutorial was run with.
Python¶
import session_info2
session_info2.session_info(dependencies=True)
scanpy prints the same report via sc.logging.print_header().
Package |
Version |
|---|---|
Python |
3.12.3 |
scanpy |
1.12 |
anndata |
0.12.19 |
numpy |
2.4.6 |
scipy |
1.18.0 |
pandas |
2.2.2 |
scikit-learn |
1.9.0 |
statsmodels |
0.14.6 |
matplotlib |
3.11.1 |
seaborn |
0.13.2 |
adjustText |
1.4.0 |
networkx |
3.6.1 |
python-igraph |
1.0.0 |
leidenalg |
0.12.0 |
liana |
1.8.1 |
decoupler |
2.2.0 |
intratalkerpy |
|
pycrosstalker |
|
deltacorrpy |
|
The last three are installed from git, so they are pinned by commit rather than by version:
pip install git+https://github.com/CostaLab/IntraTalkerpy.git@74fa5bb
pip install git+https://github.com/CostaLab/pyCrossTalkeR.git@a057b01
pip install git+https://github.com/vckraemer/deltacorrpy.git@bb249bd
deltacorrpy is pulled in by intratalkerpy; it provides the partial correlation kernel that
project_perturbation_in_embedding (step 9) runs on.
R¶
The R half — the IntraTalker/CrossTalkeR integration of step 4 and the Sankey figures of step 5 — was run with:
sessionInfo()
Package |
Version |
|---|---|
R |
4.6.0 (x86_64-pc-linux-gnu) |
Seurat |
5.5.0 |
SeuratObject |
5.4.0 |
CrossTalkeR |
2.0.0 |
LR2TF |
0.1.0 |
IntraTalker |
0.1.0 |
Matrix |
1.7.5 |
igraph |
2.3.1 |
ggraph |
2.2.2 |
ggplot2 |
4.0.3 |
ggalluvial |
0.12.6 |
dplyr |
1.2.1 |
tidyr |
1.3.2 |
scales |
1.4.0 |
colorspace |
2.1.2 |
colorBlindness |
0.1.9 |
oce |
1.8.3 |
Randomness¶
Everything that draws random numbers is seeded in the page where it runs:
Step |
Seed |
Fixes |
|---|---|---|
|
the Leiden partition and both spring layouts |
|
|
the neighbour subsampling of the embedding projection |
The MSC trajectory comes ready to use with the object of step 8, so the diffusion map and the pseudotime are the same on every run. The R half is deterministic given its input CSVs.