GPU-enabled single-cell analysis base image (Python + R) for Scanpy / scvi-tools / Seurat v5 / Monocle 3 workflows.
See tags.yaml for published versions.
Docker Hub
export DOCKERHUB_USER=abidabrar
./build.sh 1.1.0 dockerhubGitHub Container Registry (GHCR)
export GH_USER=abidabrar-bracu
# login once: echo $GH_TOKEN | docker login ghcr.io -u $GH_USER --password-stdin
./build.sh 1.1.0 ghcrLocal Build
./build.sh 1.1.0 localExample 1: bind current directory to /workspace
docker run --gpus all -it \
-p 8888:8888 \
-v "$PWD":/workspace -w /workspace \
abidabrar/scanalysis-base:1.1.0
# then inside:
# jupyter lab --ip=0.0.0.0 --no-browser --port=8888Example 2: bind code + data separately:
docker run --gpus all -it \
-p 8888:8888 \
-v /path/to/code:/workspace -w /workspace \
-v /path/to/data:/workspace/data \
abidabrar/scanalysis-base:1.1.0Note
The image creates /workspace and assigns it to the non-root vscode user for consistent write access. If you’re on Apple Silicon and see an arch warning, add --platform linux/amd64.
# Docker Hub
singularity pull scanalysis-base.sif docker://abidabrar/scanalysis-base:latestTip
put SIFs in a shared location (e.g., /mount/USER/containers/).
You can set export SINGULARITY_CACHEDIR=/path/to/big/scratch to avoid home-quota limitation.
# Get a compute node
salloc --cpus-per-task=8 --mem=32G
# or with GPU:
# salloc --cpus-per-task=8 --mem=32G --partition=gpu --constraint=rtx5000 --gres=gpu:1
# Inside the allocation:
cd /path/to/project
# Bind code and (optionally) data, enable GPUs with --nv
singularity exec --nv \
-B $PWD:/workspace \
-B /path/to/data:/workspace/data \
scanalysis-base_1.1.0.sif \
bash
# Now you'are inside the container:
# python / R / jupyter available hereNote
Add --cleanenv if local modules or environment variables interfere.
Use multiple -B flags to bind extra paths as needed.
Use the following commands as examples and put them into your Slurm job scripts, just like you would to run. Python/R nomrally.
singularity exec --nv \
-B $PWD:/workspace \
-B /path/to/data:/workspace/data \
scanalysis-base_1.0.0.sif \
python scripts/analyze.py --config /workspace/data/conf.yamlsingularity exec --nv \
-B $PWD:/workspace \
scanalysis-base_1.0.0.sif \
Rscript scripts/analysis.R- Start Jupyter inside the container:
# first get an interactive slurm job
salloc --cpus-per-task=8 --mem=32G --partition=gpu --constraint=rtx5000 --gres=gpu:1
# start jupyter with port forwarding
PORT=8888
singularity exec --nv -B $PWD:/workspace scanalysis-base_1.0.0.sif \
jupyter lab --ip=0.0.0.0 --no-browser --port=$PORT- On your laptop, open a new terminal window and forward the port from
localhostthrough the login node to the compute node (replace placeholders):
# Find compute node name from the Jupyter log, e.g., compute-1-23
ssh -L 8888:compute-1-23:8888 USER@hpc.login.address
# open http://localhost:8888 or http://127.0.0.1 in your laptop browser and paste the token- Create a
jupyter.sbatchscript. Example:
#!/bin/bash
#SBATCH --job-name=jlab
#SBATCH --partition=gpu
#SBATCH --constraint=rtx5000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --time=08:00:00
#SBATCH --output=jupyter-%J.log
#SBATCH --error=jupyter-%J.log
PORT=8888
SIF="/mount/${USER}/containers/scanalysis-base_1.1.0.sif"
WORKDIR=/path/to/code
source ~/.bashrc
echo "Compute node: $(hostname)"
echo "Using port: ${PORT}"
echo "SIF: ${SIF}"
echo "Workdir: ${WORKDIR}"
singularity exec --nv -B ${WORKDIR}:/workspace ${SIF} \
jupyter lab --ip=0.0.0.0 --no-browser --port ${PORT}- Submit the job:
sbatch jupyter.sbatch- Then
squeue -u $USER→ find the node in the log (jupyter-.log) and the Jupyter URL/token.- On your laptop, tunnel as in the interactive example, using that compute node + port.
- Torch: 2.9 + CUDA 12.8
- R: CRAN 4.4 (Ubuntu Jammy)
- Python: scanpy, scvi-tools, squidpy, spatialdata, etc.
- R: Seurat (v5.3.0), SeuratObject, seurat-wrappers, Monocle 3, BPCells, anndataR, etc
AnnData changed anndata.read. If scarches import fails:
import anndata as ad
ad.read = ad.read_h5ad
import scarches # should work nowPython stack
Brotli: 1.1.0
Cython: 3.1.4
Deprecated: 1.2.18
FlowIO: 1.4.0
HeapDict: 1.0.1
Jinja2: 3.1.4
Markdown: 3.9
MarkupSafe: 2.1.5
NaiveDE: 1.2.0
PIMS: 0.7
Pint: 0.25
PubChemPy: 1.0.5
PyOpenGL: 3.1.10
PyQt5: 5.15.11
PyQt5-Qt5: 5.15.17
PyQt5_sip: 12.17.1
PySocks: 1.7.1
PyYAML: 6.0.2
Pygments: 2.18.0
QtPy: 2.4.3
Send2Trash: 1.8.3
SpatialDE: 1.1.3
Sphinx: 8.2.3
Werkzeug: 3.1.3
absl-py: 2.3.1
adjustText: 1.3.0
aiobotocore: 2.25.0
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aioitertools: 0.12.0
aiosignal: 1.4.0
alabaster: 1.0.0
anndata: 0.12.3
anndata2ri: 2.0
annotated-types: 0.7.0
annoy: 1.17.3
anyio: 4.11.0
app-model: 0.4.0
appdirs: 1.4.4
archspec: 0.2.3
argon2-cffi: 25.1.0
argon2-cffi-bindings: 25.1.0
array-api-compat: 1.12.0
arrow: 1.4.0
arviz: 0.22.0
asciitree: 0.3.3
asttokens: 2.4.1
astunparse: 1.6.3
async-lru: 2.0.5
attrs: 24.2.0
babel: 2.17.0
bbknn: 1.6.0
beautifulsoup4: 4.12.3
bleach: 6.2.0
blitzgsea: 1.3.54
boltons: 24.0.0
botocore: 1.40.49
build: 1.3.0
cachey: 0.2.1
celltypist: 1.7.1
cellxgene-census: 1.17.0
certifi: 2024.8.30
cffi: 1.17.0
chardet: 5.2.0
charset-normalizer: 3.3.2
chex: 0.1.86
click: 8.1.7
cloudpickle: 3.1.1
colorama: 0.4.6
colorcet: 3.1.0
comm: 0.2.3
conda: 24.7.1
conda-build: 24.7.1
conda-libmamba-solver: 24.7.0
conda-package-handling: 2.3.0
conda_index: 0.5.0
conda_package_streaming: 0.10.0
contourpy: 1.3.3
cycler: 0.12.1
dask: 2024.11.2
dask-expr: 1.1.19
dask-image: 2024.5.3
datashader: 0.18.2
debugpy: 1.8.17
decorator: 5.1.1
decoupler: 2.1.1
defusedxml: 0.7.1
distro: 1.9.0
dnspython: 2.6.1
docrep: 0.3.2
docstring_parser: 0.17.0
docutils: 0.21.2
equinox: 0.11.10
et_xmlfile: 2.0.0
etils: 1.13.0
exceptiongroup: 1.2.2
executing: 2.1.0
expecttest: 0.2.1
fast-array-utils: 1.2.5
fasteners: 0.20
fastjsonschema: 2.21.2
filelock: 3.15.4
flax: 0.8.4
flexcache: 0.3
flexparser: 0.4
fonttools: 4.60.1
fqdn: 1.5.1
freetype-py: 2.5.1
frozendict: 2.4.4
frozenlist: 1.8.0
fsspec: 2025.9.0
funsor: 0.4.5
gdown: 5.2.0
geopandas: 1.1.1
grpcio: 1.75.1
h11: 0.16.0
h2: 4.1.0
h5netcdf: 1.7.2
h5py: 3.15.1
harmonypy: 0.0.10
hpack: 4.0.0
hsluv: 5.0.4
httpcore: 1.0.9
httpx: 0.28.1
hyperframe: 6.0.1
hypothesis: 6.111.2
idna: 3.8
igraph: 0.11.9
imagecodecs: 2025.8.2
imageio: 2.37.0
imagesize: 1.4.1
importlib_metadata: 8.7.0
importlib_resources: 6.4.4
in-n-out: 0.2.1
inflect: 7.5.0
ipykernel: 6.30.1
ipython: 8.27.0
ipython_pygments_lexers: 1.1.1
isoduration: 20.11.0
jax: 0.4.21
jaxlib: 0.8.0
jaxopt: 0.8.5
jaxtyping: 0.3.3
jedi: 0.19.1
jmespath: 1.0.1
joblib: 1.5.2
json5: 0.12.1
jsonpatch: 1.33
jsonpointer: 3.0.0
jsonschema: 4.23.0
jsonschema-specifications: 2023.12.1
jupyter-events: 0.12.0
jupyter-lsp: 2.3.0
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyter_server: 2.17.0
jupyter_server_terminals: 0.5.3
jupyterlab: 4.4.9
jupyterlab_pygments: 0.3.0
jupyterlab_server: 2.27.3
kiwisolver: 1.4.9
lamin_utils: 0.15.0
lazy_loader: 0.4
legacy-api-wrap: 1.4.1
legendkit: 0.3.6
leidenalg: 0.10.2
liana: 1.6.1
libarchive-c: 5.1
libmambapy: 1.5.9
lief: 0.14.1
lightning: 2.5.5
lightning-utilities: 0.15.2
lineax: 0.0.4
lintrunner: 0.12.5
llvmlite: 0.45.1
locket: 1.0.0
loguru: 0.7.3
loompy: 3.0.8
magicgui: 0.10.1
makefun: 1.16.0
mamba: 1.5.9
markdown-it-py: 4.0.0
marsilea: 0.5.6
matplotlib: 3.10.7
matplotlib-inline: 0.1.7
matplotlib-scalebar: 0.9.0
mdurl: 0.1.2
menuinst: 2.1.2
mistune: 3.1.4
mizani: 0.14.2
ml_collections: 1.1.0
ml_dtypes: 0.5.3
more-itertools: 10.4.0
mpmath: 1.3.0
msgpack: 1.1.2
mudata: 0.3.2
multidict: 6.7.0
multipledispatch: 1.0.0
multiscale_spatial_image: 2.0.3
muon: 0.1.7
napari: 0.6.6
napari-console: 0.1.4
napari-matplotlib: 3.0.0
napari-plugin-engine: 0.2.0
napari-spatialdata: 0.5.7
napari-svg: 0.2.1
natsort: 8.4.0
nbclient: 0.10.2
nbconvert: 7.16.6
nbformat: 5.10.4
nest-asyncio: 1.6.0
networkx: 3.3
newick: 1.0.0
ninja: 1.11.1.1
notebook: 7.4.7
notebook_shim: 0.2.4
npe2: 0.7.9
numba: 0.62.1
numcodecs: 0.15.1
numpy: 2.1.1
numpy-groupies: 0.11.3
numpydoc: 1.9.0
numpyro: 0.15.0
nvidia-cublas-cu12: 12.1.3.1
nvidia-cuda-cupti-cu12: 12.1.105
nvidia-cuda-nvrtc-cu12: 12.1.105
nvidia-cuda-runtime-cu12: 12.1.105
nvidia-cudnn-cu12: 9.1.0.70
nvidia-cufft-cu12: 11.0.2.54
nvidia-curand-cu12: 10.3.2.106
nvidia-cusolver-cu12: 11.4.5.107
nvidia-cusparse-cu12: 12.1.0.106
nvidia-nccl-cu12: 2.20.5
nvidia-nvjitlink-cu12: 12.1.105
nvidia-nvtx-cu12: 12.1.105
ome-types: 0.6.2
ome-zarr: 0.11.1
omnipath: 1.0.12
openpyxl: 3.1.5
opt_einsum: 3.4.0
optax: 0.2.2
optree: 0.12.1
orbax-checkpoint: 0.5.16
ott-jax: 0.4.6
overrides: 7.7.0
packaging: 25.0
pandas: 2.3.3
pandocfilters: 1.5.1
param: 2.2.1
parso: 0.8.4
partd: 1.4.2
patsy: 1.0.1
pertpy: 1.0.3
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 24.2
pkginfo: 1.11.1
pkgutil_resolve_name: 1.3.10
platformdirs: 4.2.2
plotnine: 0.15.0
plottable: 0.1.5
pluggy: 1.5.0
ply: 3.11
pooch: 1.8.2
prometheus_client: 0.23.1
prompt_toolkit: 3.0.47
propcache: 0.4.1
protobuf: 6.33.0
psutil: 6.0.0
psygnal: 0.15.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
pyarrow: 21.0.0
pyarrow-hotfix: 0.7
pyconify: 0.2.1
pycosat: 0.6.6
pycparser: 2.22
pyct: 0.6.0
pydantic: 2.12.3
pydantic-compat: 0.1.2
pydantic-extra-types: 2.10.6
pydantic_core: 2.41.4
pydot: 4.0.1
pynndescent: 0.5.13
pyogrio: 0.11.1
pyomo: 6.9.5
pyparsing: 3.2.5
pyproj: 3.7.2
pyproject_hooks: 1.2.0
pyqtgraph: 0.13.7
pyro-api: 0.1.2
pyro-ppl: 1.9.1
python-dateutil: 2.9.0.post0
python-etcd: 0.4.5
python-json-logger: 4.0.0
pytorch-lightning: 2.5.5
pytz: 2024.1
pyzmq: 27.1.0
qtconsole: 5.7.0
readfcs: 2.0.1
referencing: 0.35.1
requests: 2.32.3
rfc3339-validator: 0.1.4
rfc3986-validator: 0.1.1
rich: 14.2.0
roman-numerals-py: 3.1.0
rpds-py: 0.20.0
rpy2: 3.6.4
rpy2-rinterface: 3.6.3
rpy2-robjects: 3.6.3
ruamel.yaml: 0.18.6
ruamel.yaml.clib: 0.2.8
s3fs: 2025.9.0
scArches: 0.6.1
scHPL: 1.0.3
scanpy: 1.11.4
scib: 1.1.7
scib-metrics: 0.5.7
scikit-image: 0.25.2
scikit-learn: 1.7.2
scikit-misc: 0.5.1
scipy: 1.15.3
scvelo: 0.3.3
scvi-tools: 1.4.0
seaborn: 0.13.2
session-info2: 0.2.3
setuptools: 73.0.1
shapely: 2.1.2
shellingham: 1.5.4
six: 1.16.0
slicerator: 1.1.0
sniffio: 1.3.1
snowballstemmer: 3.0.1
somacore: 1.0.29
sortedcontainers: 2.4.0
soupsieve: 2.5
sparse: 0.17.0
sparsecca: 0.3.1
spatial_image: 1.2.3
spatialdata: 0.5.0
spatialdata-io: 0.3.0
spatialdata-plot: 0.2.12
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
squidpy: 1.6.5
stack-data: 0.6.2
statsmodels: 0.14.5
superqt: 0.7.6
sympy: 1.13.2
tangram-sc: 1.0.4
tensorboard: 2.20.0
tensorboard-data-server: 0.7.2
tensorstore: 0.1.78
terminado: 0.18.1
texttable: 1.7.0
threadpoolctl: 3.6.0
tifffile: 2025.10.16
tiledbsoma: 2.1.0
tinycss2: 1.4.0
tomli_w: 1.2.0
toolz: 1.1.0
torch: 2.4.1+cu121
torchaudio: 2.4.1+cu121
torchelastic: 0.2.2
torchmetrics: 1.8.2
torchvision: 0.19.1+cu121
tornado: 6.5.2
tqdm: 4.66.5
traitlets: 5.14.3
triton: 3.0.0
truststore: 0.9.2
typeguard: 4.4.4
typer: 0.19.2
types-dataclasses: 0.6.6
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
tzlocal: 5.3.1
umap-learn: 0.5.9.post2
uri-template: 1.3.0
urllib3: 2.2.2
validators: 0.35.0
vispy: 0.15.2
wadler_lindig: 0.1.7
wcwidth: 0.2.13
webcolors: 24.11.1
webencodings: 0.5.1
websocket-client: 1.9.0
wheel: 0.44.0
wrapt: 1.17.3
xarray: 2025.10.1
xarray-dataclass: 3.0.0
xarray-datatree: 0.0.14
xarray-einstats: 0.9.1
xarray-schema: 0.0.3
xarray-spatial: 0.4.0
xsdata: 25.7
yarl: 1.22.0
zarr: 2.18.7
zipp: 3.20.1
zstandard: 0.23.0
R stack
Package Version
AnnotationDbi 1.70.0
AnnotationFilter 1.32.0
Azimuth 0.5.0
BH 1.87.0-1
BPCells 0.3.1
BSgenome 1.76.0
BSgenome.Hsapiens.UCSC.hg38 1.4.5
Biobase 2.68.0
BiocGenerics 0.54.1
BiocIO 1.18.0
BiocManager 1.30.26
BiocNeighbors 2.2.0
BiocParallel 1.42.2
BiocSingular 1.24.0
Biostrings 2.76.0
Cairo 1.6-5
CellChat 2.2.0
ComplexHeatmap 2.24.1
DBI 1.2.3
DT 0.34.0
DelayedArray 0.34.1
DelayedMatrixStats 1.30.0
Deriv 4.2.0
DirichletMultinomial 1.50.0
EnsDb.Hsapiens.v86 2.99.0
FNN 1.1.4.1
Formula 1.2-5
GenomeInfoDb 1.44.3
GenomeInfoDbData 1.2.14
GenomicAlignments 1.44.0
GenomicFeatures 1.60.0
GenomicRanges 1.60.0
GetoptLong 1.0.5
GlobalOptions 0.1.2
HDF5Array 1.36.0
IRanges 2.42.0
IRdisplay 1.1
IRkernel 1.3.2
JASPAR2020 0.99.10
KEGGREST 1.48.1
MatrixGenerics 1.20.0
MatrixModels 0.5-4
NMF 0.28
ProtGenerics 1.40.0
R.methodsS3 1.8.2
R.oo 1.27.1
R.utils 2.12.3-9009
R6 2.6.1
RANN 2.6.2
RColorBrewer 1.1-3
RCurl 1.98-1.17
ROCR 1.0-11
RSQLite 2.4.3
RSpectra 0.16-2
Rcpp 1.1.0
RcppAnnoy 0.0.22
RcppArmadillo 15.0.2-2
RcppCCTZ 0.2.13
RcppDate 0.0.6
RcppEigen 0.3.4.0.2
RcppHNSW 0.6.0
RcppInt64 0.0.5
RcppML 0.3.7
RcppRoll 0.3.1
RcppSpdlog 0.0.23
RcppTOML 0.2.3
Rdpack 2.6.4
ResidualMatrix 1.18.0
Rhdf5lib 1.30.0
RhpcBLASctl 0.23-42
Rhtslib 3.4.0
Rsamtools 2.24.1
Rtsne 0.17
S4Arrays 1.8.1
S4Vectors 0.46.0
S7 0.2.0
ScaledMatrix 1.16.0
Seurat 5.3.0
SeuratData 0.2.2.9002
SeuratDisk 0.0.0.9021
SeuratObject 5.2.1
SeuratWrappers 0.4.0
Signac 1.16.0
SingleCellExperiment 1.30.1
SoupX 1.6.2
SparseArray 1.8.1
SparseM 1.84-2
SummarizedExperiment 1.38.1
TFBSTools 1.46.0
TFMPvalue 0.0.9
UCSC.utils 1.4.0
XML 3.99-0.19
XVector 0.48.0
abind 1.4-8
anndataR 0.99.5
arrow 21.0.0.1
askpass 1.2.1
assertthat 0.2.1
assorthead 1.2.0
aws.s3 0.3.22
aws.signature 0.6.0
backports 1.5.0
base64enc 0.1-3
batchelor 1.24.0
beachmat 2.24.0
beeswarm 0.4.0
bit 4.6.0
bit64 4.6.0-1
bitops 1.0-9
blob 1.2.4
bluster 1.18.0
brew 1.0-10
brio 1.1.5
broom 1.0.10
bslib 0.9.0
caTools 1.18.3
cachem 1.1.0
callr 3.7.6
car 3.1-3
carData 3.0-5
cellranger 1.1.0
cellxgene.census 1.16.1
circlize 0.4.16
classInt 0.4-11
cli 3.6.5
clipr 0.8.0
clue 0.3-66
coda 0.19-4.1
colorspace 2.1-2
commonmark 2.0.0
corrplot 0.95
cowplot 1.2.0
cpp11 0.5.2
crayon 1.5.3
credentials 2.0.3
crosstalk 1.2.2
curl 7.0.0
data.table 1.17.8
deldir 2.0-4
desc 1.4.3
devtools 2.4.6
diffobj 0.3.6
digest 0.6.37
distributional 0.5.0
doBy 4.7.0
doParallel 1.0.17
dotCall64 1.2
downlit 0.4.4
dplyr 1.1.4
dqrng 0.4.1
e1071 1.7-16
edgeR 4.6.3
ellipsis 0.3.2
ensembldb 2.32.0
evaluate 1.0.5
fansi 1.0.6
farver 2.1.2
fastDummies 1.7.5
fastmap 1.2.0
fastmatch 1.1-6
fitdistrplus 1.2-4
fontawesome 0.5.3
foreach 1.5.2
formatR 1.14
fs 1.6.6
furrr 0.3.1
futile.logger 1.4.3
futile.options 1.0.1
future 1.67.0
future.apply 1.20.0
gargle 1.6.0
generics 0.1.4
gert 2.1.5
ggalluvial 0.12.5
ggbeeswarm 0.7.2
ggdist 3.3.3
ggforce 0.5.0
ggnetwork 0.5.14
ggplot2 4.0.0
ggpubr 0.6.2
ggrastr 1.0.2
ggrepel 0.9.6
ggridges 0.5.7
ggsci 4.0.0
ggsignif 0.6.4
gh 1.5.0
gitcreds 0.1.2
glmGamPoi 1.20.0
glmpca 0.2.0
globals 0.18.0
glue 1.8.0
goftest 1.2-3
googledrive 2.1.2
googlesheets4 1.1.2
gplots 3.2.0
gridBase 0.4-7
gridExtra 2.3
grr 0.9.5
gtable 0.3.6
gtools 3.9.5
h5mread 1.0.1
harmony 1.2.4
hdf5r 1.3.12
here 1.0.2
hexbin 1.28.5
highr 0.11
hms 1.1.4
htmltools 0.5.8.1
htmlwidgets 1.6.4
httpuv 1.6.16
httr 1.4.7
httr2 1.2.1
ica 1.0-3
ids 1.0.1
igraph 2.2.0
ini 0.3.1
irlba 2.3.5.1
isoband 0.2.7
iterators 1.0.14
jquerylib 0.1.4
jsonlite 2.0.0
kBET 0.99.6
knitr 1.50
labeling 0.4.3
lambda.r 1.2.4
later 1.4.4
lazyeval 0.2.2
leidenbase 0.1.35
lifecycle 1.0.4
limma 3.64.3
listenv 0.9.1
lme4 1.1-37
lmtest 0.9-40
locfit 1.5-9.12
magrittr 2.0.4
matrixStats 1.5.0
memoise 2.0.1
metapod 1.16.0
microbenchmark 1.5.0
mime 0.13
miniUI 0.1.2
minqa 1.2.8
modelr 0.1.11
monocle3 1.4.26
multtest 2.64.0
nanoarrow 0.7.0-1
nanotime 0.3.12
network 1.19.0
nloptr 2.2.1
numDeriv 2016.8-1.1
openssl 2.3.4
pak 0.9.0
parallelly 1.45.1
patchwork 1.3.2
pbapply 1.7-4
pbdZMQ 0.3-14
pbkrtest 0.5.5
pbmcapply 1.5.1
pheatmap 1.0.13
pillar 1.11.1
pkgbuild 1.4.8
pkgconfig 2.0.3
pkgdown 2.1.3
pkgload 1.4.1
plotly 4.11.0
plyr 1.8.9
png 0.1-8
polyclip 1.10-7
polynom 1.4-1
praise 1.0.0
presto 1.0.0
prettyunits 1.2.0
processx 3.8.6
profvis 0.4.0
progress 1.2.3
progressr 0.17.0
promises 1.3.3
proxy 0.4-27
ps 1.9.1
pscl 1.5.9
purrr 1.1.0
pwalign 1.4.0
quadprog 1.5-8
quantreg 6.1
ragg 1.5.0
rappdirs 0.3.3
rbibutils 2.3
rcmdcheck 1.4.0
readr 2.1.5
reformulas 0.4.1
registry 0.5-1
rematch 2.0.0
rematch2 2.1.2
remotes 2.5.0
repr 1.1.7
reshape2 1.4.4
restfulr 0.0.16
reticulate 1.43.0
rhdf5 2.52.1
rhdf5filters 1.20.0
rjson 0.2.23
rlang 1.1.6
rmarkdown 2.30
rngtools 1.5.2
roxygen2 7.3.3
rprojroot 2.1.1
rsample 1.3.1
rstatix 0.7.3
rstudioapi 0.17.1
rsvd 1.0.5
rtracklayer 1.68.0
rversions 3.0.0
s2 1.1.9
sass 0.4.10
scDblFinder 1.23.4
scales 1.4.0
scater 1.36.0
scattermore 1.2
scran 1.36.0
scry 1.20.0
sctransform 0.4.2
scuttle 1.18.0
seqLogo 1.74.0
sessioninfo 1.2.3
sf 1.0-21
shape 1.4.6.1
shiny 1.11.1
shinyBS 0.61.1
shinydashboard 0.7.3
shinyjs 2.1.0
slam 0.1-55
slider 0.3.2
sna 2.8
snow 0.4-4
sourcetools 0.1.7-1
sp 2.2-0
spData 2.3.4
spam 2.11-1
sparseMatrixStats 1.20.0
spatstat.data 3.1-9
spatstat.explore 3.5-3
spatstat.geom 3.6-0
spatstat.random 3.4-2
spatstat.sparse 3.1-0
spatstat.univar 3.1-4
spatstat.utils 3.2-0
spdep 1.4-1
spdl 0.0.5
speedglm 0.3-4
statmod 1.5.1
statnet.common 4.12.0
stringi 1.8.7
stringr 1.5.2
svglite 2.2.1
sys 3.4.3
systemfonts 1.3.1
tensor 1.5.1
testthat 3.2.3
textshaping 1.0.4
tibble 3.3.0
tidyr 1.3.1
tidyselect 1.2.1
tiledb 0.33.1
tiledbsoma 2.1.0
tinytex 0.57
tweenr 2.0.3
tzdb 0.5.0
units 1.0-0
urlchecker 1.0.1
usethis 3.2.1
utf8 1.2.6
uuid 1.2-1
uwot 0.2.3
vctrs 0.6.5
vipor 0.4.7
viridis 0.6.5
viridisLite 0.4.2
vroom 1.6.6
waldo 0.6.2
warp 0.2.1
whisker 0.4.1
withr 3.0.2
wk 0.9.4
xfun 0.53
xgboost 1.7.11.1
xml2 1.4.0
xopen 1.0.1
xtable 1.8-4
yaml 2.3.10
zip 2.3.3
zoo 1.8-14
KernSmooth 2.23-26
MASS 7.3-65
Matrix 1.7-4
base 4.5.1
boot 1.3-32
class 7.3-23
cluster 2.1.8.1
codetools 0.2-19
compiler 4.5.1
datasets 4.5.1
foreign 0.8-90
grDevices 4.5.1
graphics 4.5.1
grid 4.5.1
lattice 0.22-5
methods 4.5.1
mgcv 1.9-1
nlme 3.1-168
nnet 7.3-20
parallel 4.5.1
rpart 4.1.24
spatial 7.3-15
splines 4.5.1
stats 4.5.1
stats4 4.5.1
survival 3.8-3
tcltk 4.5.1
tools 4.5.1
utils 4.5.1