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environment.txt
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environment.txt
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Python Environment:
anchor-bio 1.1.1
anndata 0.8.0
appnope 0.1.3
asttokens 2.2.1
atomicwrites 1.4.1
attrs 23.1.0
backcall 0.2.0
bamnostic 1.1.8
certifi 2022.12.7
charset-normalizer 3.1.0
CITE-seq-Count 1.4.5
click 8.1.3
comm 0.1.3
contourpy 1.0.7
coverage 7.2.3
cycler 0.11.0
debugpy 1.6.6
decorator 5.1.1
dill 0.3.7
dunamai 1.16.0
episcanpy 0.4.0
exceptiongroup 1.1.1
executing 1.2.0
fbpca 1.0
flake8 6.0.0
fonttools 4.39.3
future 0.18.3
geosketch 1.2
get_version 3.5.4
gseapy 1.0.4
h5py 3.8.0
harmonypy 0.0.9
idna 3.4
igraph 0.10.4
iniconfig 2.0.0
intervaltree 3.1.0
ipykernel 6.22.0
ipython 8.12.0
ipywidgets 8.0.6
jedi 0.18.2
joblib 1.2.0
jupyter_client 8.1.0
jupyter_core 5.3.0
jupyterlab-widgets 3.0.7
kiwisolver 1.4.4
kneed 0.8.2
legacy-api-wrap 1.2
leidenalg 0.9.1
Levenshtein 0.21.1
llvmlite 0.39.1
loompy 3.0.7
matplotlib 3.7.1
matplotlib-inline 0.1.6
mccabe 0.7.0
more-itertools 10.1.0
multiprocess 0.70.15
natsort 8.3.1
nest-asyncio 1.5.6
networkx 3.0
numba 0.56.4
numpy 1.23.5
numpy-groupies 0.9.20
packaging 23.0
pandas 1.5.3
parso 0.8.3
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 22.3.1
platformdirs 3.2.0
pluggy 1.0.0
prompt-toolkit 3.0.38
psutil 5.9.4
ptyprocess 0.7.0
pure-eval 0.2.2
py 1.11.0
pybktree 1.1
pycodestyle 2.10.0
pyflakes 3.0.1
Pygments 2.14.0
pynndescent 0.5.8
pyparsing 3.0.9
pysam 0.20.0
pytest 4.1.0
pytest-cov 4.0.0
pytest-dependency 0.4.0
python-dateutil 2.8.2
python-Levenshtein 0.21.1
pytz 2023.3
pyzmq 25.0.2
rapidfuzz 3.3.0
regex 2023.8.8
requests 2.28.2
scanorama 1.7.3
scanpy 1.9.3
scikit-learn 1.2.2
scipy 1.10.1
scvelo 0.2.5
seaborn 0.12.2
session-info 1.0.0
setuptools 65.5.0
setuptools-scm 7.1.0
six 1.16.0
sortedcontainers 2.4.0
stack-data 0.6.2
statsmodels 0.13.5
stdlib-list 0.8.0
tbb 2021.8.0
texttable 1.6.7
threadpoolctl 3.1.0
tomli 2.0.1
tornado 6.2
tqdm 4.65.0
traitlets 5.9.0
typing_extensions 4.5.0
umap-learn 0.5.3
umi-tools 1.0.0
urllib3 1.26.15
wcwidth 0.2.6
widgetsnbextension 4.0.7
R Environment:
Version Priority
ade4 "1.7-22" NA
afex "1.2-1" NA
animation "2.7" NA
AnnotationHub "3.6.0" NA
aod "1.3.2" NA
ape "5.7-1" NA
aplot "0.1.10" NA
av "0.8.3" NA
ballgown "2.30.0" NA
base64 "2.0.1" NA
bbmle "1.0.25" NA
bdsmatrix "1.3-6" NA
beachmat "2.14.0" NA
beeswarm "0.4.0" NA
BiocNeighbors "1.16.0" NA
BiocSingular "1.14.0" NA
BiocStyle "2.26.0" NA
blme "1.0-5" NA
bookdown "0.33" NA
broom.mixed "0.2.9.4" NA
Cairo "1.6-0" NA
ChIPseeker "1.34.1" NA
chromVAR "1.20.2" NA
chromVARmotifs "0.2.0" NA
circlize "0.4.15" NA
CircStats "0.2-6" NA
circular "0.4-95" NA
clue "0.3-64" NA
clusterGeneration "1.3.7" NA
clusterProfiler "4.6.2" NA
ComplexHeatmap "2.14.0" NA
covr "3.6.1" NA
DelayedMatrixStats "1.20.0" NA
deMULTIplex "1.0.2" NA
dendextend "1.16.0" NA
DESeq2 "1.38.3" NA
DHARMa "0.4.6" NA
doParallel "1.0.17" NA
DOSE "3.24.2" NA
dotwhisker "0.7.4" NA
downloader "0.4" NA
dplyr "1.1.2" NA
DT "0.27" NA
effects "4.2-2" NA
emmeans "1.8.5" NA
enrichplot "1.18.3" NA
esATAC "1.20.0" NA
estimability "1.4.1" NA
ExperimentHub "2.6.0" NA
fgsea "1.24.0" NA
furrr "0.3.1" NA
gap "1.5-1" NA
gap.datasets "0.0.5" NA
gapminder "1.0.0" NA
gee "4.13-25" NA
geneplotter "1.76.0" NA
GenomeInfoDb "1.34.9" NA
GetoptLong "1.0.5" NA
ggbeeswarm "0.7.1" NA
ggfun "0.0.9" NA
ggnewscale "0.4.8" NA
ggplot2 "3.4.2" NA
ggplotify "0.1.0" NA
ggrastr "1.0.1" NA
ggrepel "0.9.3" NA
ggseqlogo "0.1" NA
ggstance "0.3.6" NA
ggtree "3.6.2" NA
gifski "1.6.6-1" NA
glmmTMB "1.1.6" NA
GlobalOptions "0.1.2" NA
GOSemSim "2.24.0" NA
graphite "1.44.0" NA
gridGraphics "0.5-1" NA
grr "0.9.5" NA
gson "0.1.0" NA
HDO.db "0.99.1" NA
hunspell "3.0.2" NA
huxtable "5.5.2" NA
hwriter "1.3.2.1" NA
igraph "1.4.2" NA
interactiveDisplayBase "1.36.0" NA
IRdisplay "1.1" NA
JASPAR2018 "1.1.1" NA
JASPAR2020 "0.99.10" NA
lmerTest "3.1-3" NA
magick "2.7.4" NA
margins "0.3.26" NA
mgcv "1.8-42" "recommended"
mitools "2.4" NA
mlmRev "1.0-8" NA
MotifDb "1.40.0" NA
motifStack "1.42.0" NA
multcomp "1.4-23" NA
MuMIn "1.47.5" NA
muscat "1.12.1" NA
mvabund "4.2.1" NA
nabor "0.5.0" NA
ndtv "0.13.3" NA
networkD3 "0.4" NA
networkDynamic "0.11.3" NA
networkLite "1.0.5" NA
org.Hs.eg.db "3.16.0" NA
org.Mm.eg.db "3.16.0" NA
pander "0.6.5" NA
parameters "0.20.2" NA
pdftools "3.3.3" NA
phangorn "2.11.1" NA
pipeFrame "1.14.0" NA
pixmap "0.4-12" NA
plotrix "3.8-2" NA
PowerGridNetworking "0.0.0.9000" NA
prediction "0.3.14" NA
prettydoc "0.4.1" NA
pscl "1.5.5" NA
qgam "1.3.4" NA
qpdf "1.3.2" NA
quadprog "1.5-8" NA
qvalue "2.30.0" NA
r2glmm "0.1.2" NA
rbibutils "2.2.13" NA
Rbowtie2 "2.4.2" NA
Rcpp "1.0.10" NA
RcppGSL "0.3.13" NA
RcppHNSW "0.4.1" NA
RcppML "0.3.7" NA
RcppThread "2.1.3" NA
RCurl "1.98-1.10" NA
Rdpack "2.4" NA
reactome.db "1.82.0" NA
ReactomePA "1.42.0" NA
remaCor "0.0.11" NA
repr "1.1.6" NA
rex "1.2.1" NA
rhdf5 "2.42.0" NA
rhdf5filters "1.10.0" NA
Rhdf5lib "1.20.0" NA
RhpcBLASctl "0.23-42" NA
rJava "1.0-6" NA
rlang "1.1.0" NA
rmarkdown "2.21" NA
rsvd "1.0.5" NA
rsvg "2.4.0" NA
RUnit "0.4.32" NA
sandwich "3.0-2" NA
ScaledMatrix "1.6.0" NA
scater "1.26.1" NA
scatterpie "0.1.8" NA
scMCA "0.2.0" NA
scRNAseq "2.12.0" NA
scuttle "1.8.4" NA
shadowtext "0.1.2" NA
ShortRead "1.56.1" NA
SingleCellExperiment "1.20.1" NA
spelling "2.2.1" NA
splitstackshape "1.4.8" NA
statmod "1.5.0" NA
stringdist "0.9.10" NA
survey "4.1-1" NA
tesseract "5.1.0" NA
texreg "1.38.6" NA
TH.data "1.1-1" NA
threejs "0.3.3" NA
tidytree "0.4.2" NA
TMB "1.9.2" NA
treeio "1.22.0" NA
tricycle "1.6.0" NA
tweedie "2.3.5" NA
TxDb.Hsapiens.UCSC.hg19.knownGene "3.2.2" NA
tximport "1.26.1" NA
tximportData "1.26.0" NA
universalmotif "1.17.0" NA
utf8 "1.2.3" NA
variancePartition "1.28.9" NA
vctrs "0.6.2" NA
VennDiagram "1.7.3" NA
vipor "0.4.5" NA
visNetwork "2.1.2" NA
webp "1.1.0" NA
yulab.utils "0.0.6" NA
zeallot "0.1.0" NA
abind "1.4-5" NA
acepack "1.4.1" NA
AER "1.2-10" NA
annotate "1.76.0" NA
AnnotationDbi "1.60.2" NA
AnnotationFilter "1.22.0" NA
AnnotationForge "1.40.1" NA
arm "1.13-1" NA
askpass "1.1" NA
assertthat "0.2.1" NA
AUC "0.3.2" NA
backports "1.4.1" NA
base "4.2.2" "base"
base64enc "0.1-3" NA
base64url "1.4" NA
BatchJobs "1.9" NA
batchtools "0.9.16" NA
BayesFactor "0.9.12-4.4" NA
bayesplot "1.10.0" NA
bayestestR "0.13.0" NA
BBmisc "1.13" NA
bench "1.1.2" NA
betareg "3.1-4" NA
BH "1.81.0-1" NA
BiasedUrn "2.0.9" NA
bife "0.7.2" NA
bigD "0.2.0" NA
biglm "0.9-2.1" NA
binGroup "2.2-1" NA
Biobase "2.58.0" NA
BiocFileCache "2.6.1" NA
BiocGenerics "0.44.0" NA
BiocIO "1.8.0" NA
BiocManager "1.30.20" NA
BiocParallel "1.32.6" NA
BiocVersion "3.16.0" NA
biomaRt "2.54.1" NA
Biostrings "2.66.0" NA
biovizBase "1.46.0" NA
bit "4.0.5" NA
bit64 "4.0.5" NA
bitops "1.0-7" NA
blavaan "0.4-7" NA
blob "1.2.4" NA
boot "1.3-28.1" "recommended"
brew "1.0-8" NA
bridgesampling "1.1-2" NA
brio "1.1.3" NA
brms "2.19.0" NA
Brobdingnag "1.2-9" NA
broom "1.0.4" NA
BSgenome "1.66.3" NA
BSgenome.Dmelanogaster.UCSC.dm3 "1.4.0" NA
BSgenome.Hsapiens.UCSC.hg19 "1.4.3" NA
BSgenome.Mmusculus.UCSC.mm10 "1.4.3" NA
bslib "0.4.2" NA
btergm "1.10.6" NA
cachem "1.0.7" NA
callr "3.7.3" NA
car "3.1-1" NA
carData "3.0-5" NA
caret "6.0-94" NA
caTools "1.18.2" NA
ccaPP "0.3.3" NA
cellranger "1.1.0" NA
censReg "0.5-36" NA
cgam "1.20" NA
checkmate "2.1.0" NA
chemometrics "1.4.2" NA
chron "2.3-60" NA
class "7.3-21" "recommended"
classInt "0.4-9" NA
cli "3.6.1" NA
clipr "0.8.0" NA
clock "0.6.1" NA
clubSandwich "0.5.8" NA
cluster "2.1.4" "recommended"
cmprsk "2.2-11" NA
CNEr "1.34.0" NA
cobs "1.3-5" NA
coda "0.19-4" NA
codetools "0.2-19" "recommended"
collapse "1.9.3" NA
colorspace "2.1-0" NA
colourpicker "1.2.0" NA
commonmark "1.9.0" NA
compiler "4.2.2" "base"
CompQuadForm "1.4.3" NA
coneproj "1.16" NA
conflicted "1.2.0" NA
contfrac "1.1-12" NA
corpcor "1.6.10" NA
correlation "0.8.3" NA
corrplot "0.92" NA
cowplot "1.1.1" NA
coxme "2.2-18.1" "optional"
cplm "0.7-10" NA
cpp11 "0.4.3" NA
crayon "1.5.2" NA
crch "1.1-1" NA
credentials "1.3.2" NA
crosstalk "1.2.0" NA
crul "1.3" NA
cubature "2.0.4.6" NA
curl "5.0.0" NA
CVXR "1.0-11" NA
CytoTRACE "0.3.3" NA
data.table "1.14.8" NA
datasets "4.2.2" "base"
datawizard "0.7.0" NA
DBI "1.1.3" NA
dbplyr "2.3.2" NA
debugme "1.1.0" NA
DelayedArray "0.24.0" NA
deldir "1.0-6" NA
DEoptim "2.2-8" NA
DEoptimR "1.0-11" NA
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