2024 Fulcher et al. Tutorial
This tutorial demonstrates the integrated analysis of single-cell RNA-seq and proteomics data using the msmu package, based on the original dataset described in Fulcher et al. (2024).
Fulcher, J. M., Markillie, L. M., Mitchell, H. D., Williams, S. M., Engbrecht, K. M., Degnan, D. J., ... & Zhu, Y. (2024). Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting. Nature Communications, 15(1), 10614.
Tutorials
Environment Setup
.python-version: 3.11
Dependencies (pyproject.toml)
[project]
name = "2024-fulcher"
requires-python = ">=3.11"
dependencies = [
"anndata>=0.12.7",
"fastprogress==1.0.3",
"ipykernel>=7.1.0",
"ipywidgets>=8.1.8",
"mofapy2>=0.7.3",
"mofax>=0.3.7",
"msmu>=0.2.6",
"mudata>=0.3.2",
"muon>=0.1.7",
"pimms-learn",
"requests>=2.32.5",
"scanpy>=1.11.5",
]
[tool.uv.sources]
pimms-learn = { git = "https://github.com/RasmussenLab/pimms.git", rev = "327a431" }
Package Versions (pip list)
Package Version
----------------------- ---------------------
anndata 0.12.7
annotated-types 0.7.0
antlr4-python3-runtime 4.9.3
appnope 0.1.4
array-api-compat 1.13.0
asttokens 3.0.1
beartype 0.22.9
biopython 1.86
blis 1.3.3
catalogue 2.0.10
category-encoders 2.9.0
certifi 2026.1.4
charset-normalizer 3.4.4
choreographer 1.2.1
click 8.3.1
cloudpathlib 0.23.0
cloudpickle 3.1.2
comm 0.2.3
confection 0.1.5
contourpy 1.3.3
cramjam 2.11.0
cycler 0.12.1
cymem 2.0.13
debugpy 1.8.19
decorator 5.2.1
donfig 0.8.1.post1
executing 2.2.1
fastai 2.8.6
fastcluster 1.3.0
fastcore 1.12.4
fastdownload 0.0.7
fastparquet 2025.12.0
fastprogress 1.0.3
fasttransform 0.0.2
filelock 3.20.3
fonttools 4.61.1
fsspec 2026.1.0
google-crc32c 1.8.0
h5py 3.15.1
idna 3.11
iniconfig 2.3.0
inmoose 0.9.1
ipykernel 7.1.0
ipython 9.9.0
ipython-pygments-lexers 1.1.1
ipywidgets 8.1.8
jedi 0.19.2
jinja2 3.1.6
joblib 1.5.3
jupyter-client 8.8.0
jupyter-core 5.9.1
jupyterlab-widgets 3.0.16
kaleido 1.2.0
kiwisolver 1.4.9
legacy-api-wrap 1.5
llvmlite 0.46.0
logistro 2.0.1
markdown-it-py 4.0.0
markupsafe 3.0.3
matplotlib 3.10.8
matplotlib-inline 0.2.1
mdurl 0.1.2
mofapy2 0.7.3
mofax 0.3.7
mpmath 1.3.0
mrmr-selection 0.2.8
msmu 0.2.6
mudata 0.3.2
muon 0.1.7
murmurhash 1.0.15
narwhals 2.15.0
natsort 8.4.0
nest-asyncio 1.6.0
networkx 3.6.1
njab 0.1.1
numba 0.63.1
numcodecs 0.16.5
numpy 2.3.5
omegaconf 2.3.0
orjson 3.11.5
packaging 26.0
pandas 2.3.3
pandas-flavor 0.8.1
parso 0.8.5
patsy 1.0.2
pexpect 4.9.0
pillow 12.1.0
pimms-learn 0.5.1.dev8+g327a431a0
pingouin 0.5.5
pip 25.3
platformdirs 4.5.1
plotly 6.5.2
pluggy 1.6.0
plum-dispatch 2.6.1
polars 1.37.1
polars-runtime-32 1.37.1
preshed 3.0.12
prompt-toolkit 3.0.52
protobuf 6.33.4
psutil 7.2.1
ptyprocess 0.7.0
pure-eval 0.2.3
pydantic 2.12.5
pydantic-core 2.41.5
pygments 2.19.2
pynndescent 0.6.0
pyopenms 3.5.0
pyparsing 3.3.2
pytest 9.0.2
pytest-timeout 2.4.0
python-dateutil 2.9.0.post0
pytz 2025.2
pyyaml 6.0.3
pyzmq 27.1.0
requests 2.32.5
rich 14.2.0
scanpy 1.11.5
scikit-learn 1.8.0
scipy 1.17.0
seaborn 0.13.2
session-info2 0.3
setuptools 80.10.1
simplejson 3.20.2
six 1.17.0
smart-open 7.5.0
spacy 3.8.11
spacy-legacy 3.0.12
spacy-loggers 1.0.5
srsly 2.5.2
stack-data 0.6.3
statsmodels 0.14.6
sympy 1.14.0
tabulate 0.9.0
thinc 8.3.10
threadpoolctl 3.6.0
torch 2.9.1
torchvision 0.24.1
tornado 6.5.4
tqdm 4.67.1
traitlets 5.14.3
typer-slim 0.21.1
typing-extensions 4.15.0
typing-inspection 0.4.2
tzdata 2025.3
umap-learn 0.5.11
urllib3 2.6.3
wasabi 1.1.3
wcwidth 0.3.1
weasel 0.4.3
widgetsnbextension 4.0.15
wrapt 2.0.1
xarray 2025.12.0
zarr 3.1.5