x86_64 default rnaseq notebook c448e27f699f - huchlab/sequencing-docker-stacks GitHub Wiki
- Build timestamp: 2025-12-05T11:03:46Z
- Docker image:
quay.io/huchlab/rnaseq-notebook:c448e27f699f - Docker image size: 11.1GB
- Git commit SHA: c448e27f699f2eabd5c60e55744f19b6045344d1
- Git commit message:
Merge pull request #428 from huchlab/copilot/add-r-clustree-package
Add r-clustree package to singlecell-notebook
Python 3.13.10
conda info:
active environment : None
user config file : /home/jovyan/.condarc
populated config files : /opt/conda/.condarc
/home/jovyan/.condarc
conda version : 25.11.0
conda-build version : not installed
python version : 3.13.10.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen2
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base environment : /opt/conda (writable)
conda av data dir : /opt/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
package cache : /opt/conda/pkgs
/home/jovyan/.conda/pkgs
envs directories : /opt/conda/envs
/home/jovyan/.conda/envs
platform : linux-64
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UID:GID : 1000:100
netrc file : None
offline mode : False
mamba info:
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mamba version : 2.4.0
curl version : libcurl/8.17.0 OpenSSL/3.6.0 zlib/1.3.1 zstd/1.5.7 libssh2/1.11.1 nghttp2/1.67.0 mit-krb5/1.21.3
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envs directories : /opt/conda/envs
package cache : /opt/conda/pkgs
/home/jovyan/.mamba/pkgs
environment : base
env location : /opt/conda
user config files : /home/jovyan/.mambarc
populated config files : /home/jovyan/.condarc
/opt/conda/.condarc
virtual packages : __unix=0=0
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channels : https://conda.anaconda.org/conda-forge/linux-64
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base environment : /opt/conda
platform : linux-64
mamba list:
List of packages in environment: "/opt/conda"
Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────────────────
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r-later 1.4.4 r44h3697838_1 conda-forge
r-lattice 0.22_7 r44h54b55ab_1 conda-forge
r-latticeextra 0.6_31 r44hc72bb7e_0 conda-forge
r-lava 1.8.2 r44hc72bb7e_0 conda-forge
r-lazyeval 0.2.2 r44h54b55ab_6 conda-forge
r-lhs 1.2.0 r44h3697838_1 conda-forge
r-lifecycle 1.0.4 r44hc72bb7e_2 conda-forge
r-lintr 3.3.0_1 r44hc72bb7e_0 conda-forge
r-listenv 0.10.0 r44hc72bb7e_0 conda-forge
r-lme4 1.1_38 r44h3697838_0 conda-forge
r-lmertest 3.1_3 r44hc72bb7e_4 conda-forge
r-lmtest 0.9_40 r44heaba542_4 conda-forge
r-locfit 1.5_9.12 r44h54b55ab_1 conda-forge
r-lubridate 1.9.4 r44h54b55ab_1 conda-forge
r-magick 2.9.0 r44h3697838_1 conda-forge
r-magrittr 2.0.4 r44h54b55ab_0 conda-forge
r-mass 7.3_65 r44h54b55ab_0 conda-forge
r-matrix 1.7_4 r44h0e4624f_1 conda-forge
r-matrixmodels 0.5_4 r44hc72bb7e_1 conda-forge
r-matrixstats 1.5.0 r44h54b55ab_1 conda-forge
r-memoise 2.0.1 r44hc72bb7e_4 conda-forge
r-mgcv 1.9_4 r44h0e4624f_0 conda-forge
r-microbenchmark 1.5.0 r44h54b55ab_1 conda-forge
r-mime 0.13 r44h54b55ab_1 conda-forge
r-miniui 0.1.2 r44hc72bb7e_1 conda-forge
r-minqa 1.2.8 r44ha36cffa_2 conda-forge
r-mixsqp 0.3_54 r44h3704496_4 conda-forge
r-modeldata 1.5.1 r44hc72bb7e_1 conda-forge
r-modelenv 0.2.0 r44hc72bb7e_1 conda-forge
r-modelmetrics 1.2.2.2 r44h3697838_5 conda-forge
r-modelr 0.1.11 r44hc72bb7e_3 conda-forge
r-munsell 0.5.1 r44hc72bb7e_2 conda-forge
r-mvtnorm 1.3_3 r44h11cdb10_1 conda-forge
r-nlme 3.1_168 r44heaba542_1 conda-forge
r-nloptr 2.2.1 r44h8ae9fae_1 conda-forge
r-nnet 7.3_20 r44h54b55ab_1 conda-forge
r-nortest 1.0_4 r44hc72bb7e_1007 conda-forge
r-numderiv 2016.8_1.1 r44hc72bb7e_7 conda-forge
r-nycflights13 1.0.2 r44h785f33e_5 conda-forge
r-openssl 2.3.4 r44h50f7d53_0 conda-forge
r-openxlsx 4.2.8.1 r44h3697838_0 conda-forge
r-otel 0.2.0 r44hc72bb7e_1 conda-forge
r-paletteer 1.6.0 r44h785f33e_2 conda-forge
r-paralleldist 0.2.7 r44h3704496_1 conda-forge
r-parallelly 1.45.1 r44h54b55ab_1 conda-forge
r-parsnip 1.4.0 r44hc72bb7e_0 conda-forge
r-patchwork 1.3.2 r44hc72bb7e_1 conda-forge
r-pbdzmq 0.3_14 r44hded8526_1 conda-forge
r-pbkrtest 0.5.5 r44hc72bb7e_1 conda-forge
r-pheatmap 1.0.13 r44hc72bb7e_1 conda-forge
r-pillar 1.11.1 r44hc72bb7e_0 conda-forge
r-pkgbuild 1.4.8 r44hc72bb7e_1 conda-forge
r-pkgconfig 2.0.3 r44hc72bb7e_5 conda-forge
r-pkgdown 2.2.0 r44hc72bb7e_0 conda-forge
r-pkgload 1.4.1 r44hc72bb7e_0 conda-forge
r-plogr 0.2.0 r44hc72bb7e_1007 conda-forge
r-plotly 4.11.0 r44hc72bb7e_1 conda-forge
r-plyr 1.8.9 r44h3697838_3 conda-forge
r-png 0.1_8 r44h6b2d295_3 conda-forge
r-polyclip 1.10_7 r44h3697838_1 conda-forge
r-polynom 1.4_1 r44hc72bb7e_4 conda-forge
r-praise 1.0.0 r44hc72bb7e_1009 conda-forge
r-prettyunits 1.2.0 r44hc72bb7e_2 conda-forge
r-prismatic 1.1.2 r44hc72bb7e_2 conda-forge
r-proc 1.19.0.1 r44h3697838_1 conda-forge
r-processx 3.8.6 r44h54b55ab_1 conda-forge
r-prodlim 2025.04.28 r44h3697838_1 conda-forge
r-profvis 0.4.0 r44h54b55ab_1 conda-forge
r-progress 1.2.3 r44hc72bb7e_2 conda-forge
r-progressr 0.18.0 r44hc72bb7e_0 conda-forge
r-promises 1.5.0 r44hc72bb7e_1 conda-forge
r-proxy 0.4_27 r44h54b55ab_4 conda-forge
r-ps 1.9.1 r44h54b55ab_1 conda-forge
r-purrr 1.2.0 r44h54b55ab_0 conda-forge
r-quadprog 1.5_8 r44ha0a88a1_7 conda-forge
r-quantmod 0.4.28 r44hc72bb7e_1 conda-forge
r-quantreg 6.1 r44h11cdb10_1 conda-forge
r-r.cache 0.17.0 r44hc72bb7e_1 conda-forge
r-r.methodss3 1.8.2 r44hc72bb7e_4 conda-forge
r-r.oo 1.27.1 r44hc72bb7e_1 conda-forge
r-r.utils 2.13.0 r44hc72bb7e_1 conda-forge
r-r6 2.6.1 r44hc72bb7e_1 conda-forge
r-ragg 1.5.0 r44h9f1dc4d_1 conda-forge
r-randomforest 4.7_1.2 r44heaba542_1 conda-forge
r-rappdirs 0.3.3 r44h54b55ab_4 conda-forge
r-rbibutils 2.4 r44h54b55ab_0 conda-forge
r-rcmdcheck 1.4.0 r44h785f33e_4 conda-forge
r-rcolorbrewer 1.1_3 r44h785f33e_4 conda-forge
r-rcpp 1.1.0 r44h3697838_1 conda-forge
r-rcpparmadillo 15.2.2_1 r44h3704496_0 conda-forge
r-rcppeigen 0.3.4.0.2 r44h3704496_1 conda-forge
r-rcppnumerical 0.6_0 r44h3697838_2 conda-forge
r-rcppparallel 5.1.11_1 r44h0d96847_4 conda-forge
r-rcurl 1.98_1.17 r44h46721d4_2 conda-forge
r-rdpack 2.6.4 r44hc72bb7e_1 conda-forge
r-readr 2.1.6 r44h3697838_0 conda-forge
r-readxl 1.4.5 r44h10e25cc_1 conda-forge
r-recipes 1.3.1 r44hc72bb7e_1 conda-forge
r-reformulas 0.4.2 r44hc72bb7e_0 conda-forge
r-remacor 0.0.20 r44h3704496_1 conda-forge
r-rematch 2.0.0 r44hc72bb7e_2 conda-forge
r-rematch2 2.1.2 r44hc72bb7e_5 conda-forge
r-remotes 2.5.0 r44hc72bb7e_2 conda-forge
r-repr 1.1.7 r44h785f33e_2 conda-forge
r-reprex 2.1.1 r44hc72bb7e_2 conda-forge
r-reshape2 1.4.5 r44h3697838_0 conda-forge
r-restfulr 0.0.16 r44h5ef9028_0 bioconda
r-rex 1.2.1 r44hc72bb7e_4 conda-forge
r-rhpcblasctl 0.23_42 r44h54b55ab_4 conda-forge
r-rjson 0.2.23 r44h3697838_1 conda-forge
r-rlang 1.1.6 r44h3697838_1 conda-forge
r-rmarkdown 2.30 r44hc72bb7e_0 conda-forge
r-robustrankaggreg 1.2.1 r44hc72bb7e_4 conda-forge
r-rodbc 1.3_26 r44h54b55ab_1 conda-forge
r-roxygen2 7.3.3 r44h3697838_1 conda-forge
r-rpart 4.1.24 r44h54b55ab_1 conda-forge
r-rprojroot 2.1.1 r44hc72bb7e_1 conda-forge
r-rsample 1.3.1 r44hc72bb7e_1 conda-forge
r-rsqlite 2.4.5 r44h3697838_0 conda-forge
r-rstatix 0.7.3 r44hc72bb7e_0 conda-forge
r-rstudioapi 0.17.1 r44hc72bb7e_1 conda-forge
r-rsvd 1.0.5 r44hc72bb7e_3 conda-forge
r-rversions 3.0.0 r44hc72bb7e_0 conda-forge
r-rvest 1.0.5 r44hc72bb7e_1 conda-forge
r-s7 0.2.1 r44h54b55ab_0 conda-forge
r-sass 0.4.10 r44h3697838_1 conda-forge
r-scales 1.4.0 r44hc72bb7e_1 conda-forge
r-scatterpie 0.2.6 r44hc72bb7e_1 conda-forge
r-selectr 0.5_0 r44hc72bb7e_0 conda-forge
r-sessioninfo 1.2.3 r44hc72bb7e_1 conda-forge
r-sfd 0.1.0 r44hc72bb7e_2 conda-forge
r-shape 1.4.6.1 r44ha770c72_2 conda-forge
r-shiny 1.12.0 r44h785f33e_0 conda-forge
r-slider 0.3.3 r44h3697838_0 conda-forge
r-snakecase 0.11.1 r44hc72bb7e_2 conda-forge
r-snow 0.4_4 r44hc72bb7e_4 conda-forge
r-sourcetools 0.1.7_1 r44h3697838_3 conda-forge
r-sparsem 1.84_2 r44heaba542_1 conda-forge
r-sparsevctrs 0.3.4 r44h54b55ab_1 conda-forge
r-squarem 2021.1 r44hc72bb7e_4 conda-forge
r-statmod 1.5.1 r44hb1d0f04_0 conda-forge
r-strawr 0.0.92 r44h09def59_3 conda-forge
r-stringi 1.8.7 r44h2dae267_1 conda-forge
r-stringr 1.6.0 r44h785f33e_0 conda-forge
r-styler 1.11.0 r44hc72bb7e_0 conda-forge
r-survival 3.8_3 r44h54b55ab_1 conda-forge
r-svglite 2.2.2 r44h8ff94db_0 conda-forge
r-sys 3.4.3 r44h54b55ab_1 conda-forge
r-systemfonts 1.3.1 r44h74f4acd_0 conda-forge
r-tailor 0.1.0 r44hc72bb7e_1 conda-forge
r-testthat 3.3.1 r44h3697838_0 conda-forge
r-textshaping 1.0.4 r44h74f4acd_0 conda-forge
r-tibble 3.3.0 r44h54b55ab_1 conda-forge
r-tidygraph 1.3.0 r44h3697838_2 conda-forge
r-tidymodels 1.4.1 r44h785f33e_1 conda-forge
r-tidyr 1.3.1 r44h3697838_2 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_2 conda-forge
r-tidytree 0.4.6 r44hc72bb7e_2 conda-forge
r-tidyverse 2.0.0 r44h785f33e_3 conda-forge
r-timechange 0.3.0 r44h3697838_2 conda-forge
r-timedate 4051.111 r44hc72bb7e_0 conda-forge
r-tinytex 0.58 r44hc72bb7e_0 conda-forge
r-truncnorm 1.0_9 r44h54b55ab_5 conda-forge
r-tseries 0.10_58 r44ha0a88a1_1 conda-forge
r-ttr 0.24.4 r44h54b55ab_2 conda-forge
r-tune 2.0.1 r44hc72bb7e_0 conda-forge
r-tweenr 2.0.3 r44h3697838_2 conda-forge
r-tzdb 0.5.0 r44h3697838_2 conda-forge
r-urca 1.3_4 r44heaba542_2 conda-forge
r-urlchecker 1.0.1 r44hc72bb7e_4 conda-forge
r-usethis 3.2.1 r44hc72bb7e_1 conda-forge
r-utf8 1.2.6 r44h54b55ab_1 conda-forge
r-uuid 1.2_1 r44h54b55ab_1 conda-forge
r-vctrs 0.6.5 r44h3697838_2 conda-forge
r-viridis 0.6.5 r44hc72bb7e_2 conda-forge
r-viridislite 0.4.2 r44hc72bb7e_3 conda-forge
r-vroom 1.6.7 r44h3697838_0 conda-forge
r-waldo 0.6.2 r44hc72bb7e_1 conda-forge
r-warp 0.2.2 r44h54b55ab_0 conda-forge
r-whisker 0.4.1 r44hc72bb7e_3 conda-forge
r-withr 3.0.2 r44hc72bb7e_1 conda-forge
r-workflows 1.3.0 r44hc72bb7e_1 conda-forge
r-workflowsets 1.1.1 r44h785f33e_1 conda-forge
r-writexl 1.5.4 r44h1c8cec4_1 conda-forge
r-xfun 0.54 r44h3697838_0 conda-forge
r-xml 3.99_0.20 r44hf705907_0 conda-forge
r-xml2 1.5.0 r44he78afff_0 conda-forge
r-xmlparsedata 1.0.5 r44hc72bb7e_4 conda-forge
r-xopen 1.0.1 r44hc72bb7e_2 conda-forge
r-xtable 1.8_4 r44hc72bb7e_7 conda-forge
r-xts 0.14.1 r44h54b55ab_1 conda-forge
r-yaml 2.3.11 r44h54b55ab_0 conda-forge
r-yardstick 1.3.2 r44h54b55ab_1 conda-forge
r-yulab.utils 0.2.2 r44hc72bb7e_0 conda-forge
r-zip 2.3.3 r44h54b55ab_1 conda-forge
r-zoo 1.8_14 r44h54b55ab_1 conda-forge
rav1e 0.7.1 h8fae777_3 conda-forge
re2 2025.11.05 h5301d42_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
reproc 14.2.5.post0 hb9d3cd8_0 conda-forge
reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
requests-cache 0.4.13 pypi_0 pypi
requests_cache 0.4.13 py_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rfc3987-syntax 1.1.0 pyhe01879c_1 conda-forge
rpds-py 0.30.0 py313h843e2db_0 conda-forge
rpy2 3.6.4 py313r44h67dc6d7_1 conda-forge
ruamel.yaml 0.18.16 py313h07c4f96_0 conda-forge
ruamel.yaml.clib 0.2.14 py313h07c4f96_0 conda-forge
s2n 1.6.0 h8399546_1 conda-forge
scikit-image 0.25.2 py313h08cd8bf_2 conda-forge
scikit-learn 1.7.2 py313h06d4379_0 conda-forge
scipy 1.16.3 py313h11c21cd_1 conda-forge
seaborn 0.13.2 hd8ed1ab_3 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
sed 4.9 h6688a6e_0 conda-forge
send2trash 1.8.3 pyh0d859eb_1 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
session-info2 0.2.3 pyhd8ed1ab_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
simdjson 4.2.2 hb700be7_0 conda-forge
simpervisor 1.0.0 pyhd8ed1ab_1 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snappy 1.2.2 h03e3b7b_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_2 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_1 conda-forge
soupsieve 2.8 pyhd8ed1ab_0 conda-forge
sqlalchemy 2.0.44 py313h07c4f96_0 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.5 py313h29aa505_1 conda-forge
stdlib-list 0.12.0 pyhd8ed1ab_0 conda-forge
svt-av1 3.1.2 hecca717_0 conda-forge
sympy 1.14.0 pyh2585a3b_105 conda-forge
sysroot_linux-64 2.39 hc4b9eeb_3 conda-forge
tbb 2022.3.0 h8d10470_1 conda-forge
tbb-devel 2022.3.0 h74b38a2_1 conda-forge
tblib 3.2.2 pyhcf101f3_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tifffile 2025.10.16 pyhd8ed1ab_0 conda-forge
tinycss2 1.5.1 pyhcf101f3_0 conda-forge
tk 8.6.13 noxft_ha0e22de_103 conda-forge
tktable 2.10 h8d826fa_7 conda-forge
toml 0.10.2 pyhcf101f3_3 conda-forge
tomli 2.3.0 pyhcf101f3_0 conda-forge
tomlkit 0.13.3 pyha770c72_0 conda-forge
toolz 1.1.0 pyhd8ed1ab_1 conda-forge
tornado 6.5.2 py313h07c4f96_2 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
truststore 0.10.3 pyhe01879c_0 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.2 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
tzlocal 5.3.1 pyh8f84b5b_0 conda-forge
unixodbc 2.3.14 h69e2008_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
uv 0.9.15 h76e24b7_0 conda-forge
wayland 1.24.0 hd6090a7_1 conda-forge
wcwidth 0.2.14 pyhd8ed1ab_0 conda-forge
webcolors 25.10.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.9.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.15 pyhd8ed1ab_0 conda-forge
x265 3.5 h924138e_3 conda-forge
xkeyboard-config 2.46 hb03c661_0 conda-forge
xlrd 2.0.2 pyhd8ed1ab_0 conda-forge
xmltodict 1.0.2 pyhcf101f3_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxcomposite 0.4.6 hb9d3cd8_2 conda-forge
xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.2 hb03c661_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxinerama 1.1.5 h5888daf_1 conda-forge
xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xorg-libxxf86vm 1.1.6 hb9d3cd8_0 conda-forge
xorg-xorgproto 2024.1 hb9d3cd8_1 conda-forge
xyzservices 2025.11.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yaml-cpp 0.8.0 h3f2d84a_0 conda-forge
yarl 1.22.0 py313h3dea7bd_0 conda-forge
yq 3.4.3 pyhe01879c_2 conda-forge
zeromq 4.3.5 h387f397_9 conda-forge
zfp 1.0.1 h909a3a2_3 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.23.0 pyhcf101f3_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.3.2 h54a6638_0 conda-forge
zstandard 0.25.0 py313h54dd161_1 conda-forge
zstd 1.5.7 h3691f8a_5 conda-forge
apt list --installed:
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Listing...
adduser/now 3.137ubuntu1 all [installed,local]
apt/now 2.8.3 amd64 [installed,local]
base-files/now 13ubuntu10.3 amd64 [installed,local]
base-passwd/now 3.6.3build1 amd64 [installed,local]
bash/now 5.2.21-2ubuntu4 amd64 [installed,local]
binutils-common/now 2.42-4ubuntu2.7 amd64 [installed,local]
binutils-x86-64-linux-gnu/now 2.42-4ubuntu2.7 amd64 [installed,local]
binutils/now 2.42-4ubuntu2.7 amd64 [installed,local]
bsdutils/now 1:2.39.3-9ubuntu6.3 amd64 [installed,local]
build-essential/now 12.10ubuntu1 amd64 [installed,local]
bzip2/now 1.0.8-5.1build0.1 amd64 [installed,local]
ca-certificates/now 20240203 all [installed,local]
cm-super-minimal/now 0.3.4-17 all [installed,local]
cm-super/now 0.3.4-17 all [installed,local]
coreutils/now 9.4-3ubuntu6.1 amd64 [installed,local]
cpp-13-x86-64-linux-gnu/now 13.3.0-6ubuntu2~24.04 amd64 [installed,local]
cpp-13/now 13.3.0-6ubuntu2~24.04 amd64 [installed,local]
cpp-x86-64-linux-gnu/now 4:13.2.0-7ubuntu1 amd64 [installed,local]
cpp/now 4:13.2.0-7ubuntu1 amd64 [installed,local]
curl/now 8.5.0-2ubuntu10.6 amd64 [installed,local]
dash/now 0.5.12-6ubuntu5 amd64 [installed,local]
debconf/now 1.5.86ubuntu1 all [installed,local]
debianutils/now 5.17build1 amd64 [installed,local]
diffutils/now 1:3.10-1build1 amd64 [installed,local]
dpkg-dev/now 1.22.6ubuntu6.5 all [installed,local]
dpkg/now 1.22.6ubuntu6.5 amd64 [installed,local]
dvipng/now 1.15-1.1 amd64 [installed,local]
e2fsprogs/now 1.47.0-2.4~exp1ubuntu4.1 amd64 [installed,local]
ffmpeg/now 7:6.1.1-3ubuntu5 amd64 [installed,local]
findutils/now 4.9.0-5build1 amd64 [installed,local]
fontconfig-config/now 2.15.0-1.1ubuntu2 amd64 [installed,local]
fontconfig/now 2.15.0-1.1ubuntu2 amd64 [installed,local]
fonts-dejavu-core/now 2.37-8 all [installed,local]
fonts-dejavu-extra/now 2.37-8 all [installed,local]
fonts-dejavu-mono/now 2.37-8 all [installed,local]
fonts-dejavu/now 2.37-8 all [installed,local]
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libudev1/now 255.4-1ubuntu8.11 amd64 [installed,local]
libudfread0/now 1.1.2-1build1 amd64 [installed,local]
libunibreak5/now 5.1-2build1 amd64 [installed,local]
libunistring5/now 1.1-2build1.1 amd64 [installed,local]
libusb-1.0-0/now 2:1.0.27-1 amd64 [installed,local]
libuuid1/now 2.39.3-9ubuntu6.3 amd64 [installed,local]
libva-drm2/now 2.20.0-2build1 amd64 [installed,local]
libva-x11-2/now 2.20.0-2build1 amd64 [installed,local]
libva2/now 2.20.0-2build1 amd64 [installed,local]
libvdpau1/now 1.5-2build1 amd64 [installed,local]
libvidstab1.1/now 1.1.0-2build1 amd64 [installed,local]
libvorbis0a/now 1.3.7-1build3 amd64 [installed,local]
libvorbisenc2/now 1.3.7-1build3 amd64 [installed,local]
libvorbisfile3/now 1.3.7-1build3 amd64 [installed,local]
libvpl2/now 2023.3.0-1build1 amd64 [installed,local]
libvpx9/now 1.14.0-1ubuntu2.2 amd64 [installed,local]
libvulkan1/now 1.3.275.0-1build1 amd64 [installed,local]
libwayland-client0/now 1.22.0-2.1build1 amd64 [installed,local]
libwayland-cursor0/now 1.22.0-2.1build1 amd64 [installed,local]
libwayland-egl1/now 1.22.0-2.1build1 amd64 [installed,local]
libwayland-server0/now 1.22.0-2.1build1 amd64 [installed,local]
libwebp7/now 1.3.2-0.4build3 amd64 [installed,local]
libwebpmux3/now 1.3.2-0.4build3 amd64 [installed,local]
libx11-6/now 2:1.8.7-1build1 amd64 [installed,local]
libx11-data/now 2:1.8.7-1build1 all [installed,local]
libx11-xcb1/now 2:1.8.7-1build1 amd64 [installed,local]
libx264-164/now 2:0.164.3108+git31e19f9-1 amd64 [installed,local]
libx265-199/now 3.5-2build1 amd64 [installed,local]
libxau6/now 1:1.0.9-1build6 amd64 [installed,local]
libxaw7/now 2:1.0.14-1build2 amd64 [installed,local]
libxcb-dri3-0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-glx0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-present0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-randr0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-render0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-shape0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-shm0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-sync1/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb-xfixes0/now 1.15-1ubuntu2 amd64 [installed,local]
libxcb1/now 1.15-1ubuntu2 amd64 [installed,local]
libxcursor1/now 1:1.2.1-1build1 amd64 [installed,local]
libxdmcp6/now 1:1.1.3-0ubuntu6 amd64 [installed,local]
libxext6/now 2:1.3.4-1build2 amd64 [installed,local]
libxfixes3/now 1:6.0.0-2build1 amd64 [installed,local]
libxi6/now 2:1.8.1-1build1 amd64 [installed,local]
libxkbcommon0/now 1.6.0-1build1 amd64 [installed,local]
libxml2/now 2.9.14+dfsg-1.3ubuntu3.6 amd64 [installed,local]
libxmu6/now 2:1.1.3-3build2 amd64 [installed,local]
libxpm4/now 1:3.5.17-1build2 amd64 [installed,local]
libxrandr2/now 2:1.5.2-2build1 amd64 [installed,local]
libxrender1/now 1:0.9.10-1.1build1 amd64 [installed,local]
libxshmfence1/now 1.3-1build5 amd64 [installed,local]
libxss1/now 1:1.2.3-1build3 amd64 [installed,local]
libxt6t64/now 1:1.2.1-1.2build1 amd64 [installed,local]
libxv1/now 2:1.0.11-1.1build1 amd64 [installed,local]
libxvidcore4/now 2:1.3.7-1build1 amd64 [installed,local]
libxxf86vm1/now 1:1.1.4-1build4 amd64 [installed,local]
libxxhash0/now 0.8.2-2build1 amd64 [installed,local]
libyaml-0-2/now 0.2.5-1build1 amd64 [installed,local]
libzimg2/now 3.0.5+ds1-1build1 amd64 [installed,local]
libzix-0-0/now 0.4.2-2build1 amd64 [installed,local]
libzmq5/now 4.3.5-1build2 amd64 [installed,local]
libzstd1/now 1.5.5+dfsg2-2build1.1 amd64 [installed,local]
libzvbi-common/now 0.2.42-2 all [installed,local]
libzvbi0t64/now 0.2.42-2 amd64 [installed,local]
libzzip-0-13t64/now 0.13.72+dfsg.1-1.2build1 amd64 [installed,local]
linux-libc-dev/now 6.8.0-88.89 amd64 [installed,local]
locales/now 2.39-0ubuntu8.6 all [installed,local]
login/now 1:4.13+dfsg1-4ubuntu3.2 amd64 [installed,local]
logsave/now 1.47.0-2.4~exp1ubuntu4.1 amd64 [installed,local]
lto-disabled-list/now 47 all [installed,local]
make/now 4.3-4.1build2 amd64 [installed,local]
mawk/now 1.3.4.20240123-1build1 amd64 [installed,local]
media-types/now 10.1.0 all [installed,local]
mesa-libgallium/now 25.0.7-0ubuntu0.24.04.2 amd64 [installed,local]
mount/now 2.39.3-9ubuntu6.3 amd64 [installed,local]
nano-tiny/now 7.2-2ubuntu0.1 amd64 [installed,local]
ncurses-base/now 6.4+20240113-1ubuntu2 all [installed,local]
ncurses-bin/now 6.4+20240113-1ubuntu2 amd64 [installed,local]
netbase/now 6.4 all [installed,local]
ocl-icd-libopencl1/now 2.3.2-1build1 amd64 [installed,local]
openssh-client/now 1:9.6p1-3ubuntu13.14 amd64 [installed,local]
openssl/now 3.0.13-0ubuntu3.6 amd64 [installed,local]
pandoc-data/now 3.1.3-1 all [installed,local]
pandoc/now 3.1.3+ds-2 amd64 [installed,local]
passwd/now 1:4.13+dfsg1-4ubuntu3.2 amd64 [installed,local]
patch/now 2.7.6-7build3 amd64 [installed,local]
perl-base/now 5.38.2-3.2ubuntu0.2 amd64 [installed,local]
perl-modules-5.38/now 5.38.2-3.2ubuntu0.2 all [installed,local]
perl/now 5.38.2-3.2ubuntu0.2 amd64 [installed,local]
pfb2t1c2pfb/now 0.3-11build1 amd64 [installed,local]
poppler-data/now 0.4.12-1 all [installed,local]
preview-latex-style/now 13.2-1 all [installed,local]
procps/now 2:4.0.4-4ubuntu3.2 amd64 [installed,local]
python3-minimal/now 3.12.3-0ubuntu2.1 amd64 [installed,local]
python3.12-minimal/now 3.12.3-1ubuntu0.9 amd64 [installed,local]
python3.12/now 3.12.3-1ubuntu0.9 amd64 [installed,local]
python3/now 3.12.3-0ubuntu2.1 amd64 [installed,local]
readline-common/now 8.2-4build1 all [installed,local]
rpcsvc-proto/now 1.4.2-0ubuntu7 amd64 [installed,local]
run-one/now 1.17-0ubuntu2 all [installed,local]
sed/now 4.9-2build1 amd64 [installed,local]
sensible-utils/now 0.0.22 all [installed,local]
shared-mime-info/now 2.4-4 amd64 [installed,local]
sudo/now 1.9.15p5-3ubuntu5.24.04.1 amd64 [installed,local]
sysvinit-utils/now 3.08-6ubuntu3 amd64 [installed,local]
t1utils/now 1.41-4build3 amd64 [installed,local]
tar/now 1.35+dfsg-3build1 amd64 [installed,local]
teckit/now 2.5.12+ds1-1 amd64 [installed,local]
tex-common/now 6.18 all [installed,local]
texlive-base/now 2023.20240207-1 all [installed,local]
texlive-binaries/now 2023.20230311.66589-9build3 amd64 [installed,local]
texlive-fonts-recommended/now 2023.20240207-1 all [installed,local]
texlive-latex-base/now 2023.20240207-1 all [installed,local]
texlive-latex-extra/now 2023.20240207-1 all [installed,local]
texlive-latex-recommended/now 2023.20240207-1 all [installed,local]
texlive-pictures/now 2023.20240207-1 all [installed,local]
texlive-plain-generic/now 2023.20240207-1 all [installed,local]
texlive-xetex/now 2023.20240207-1 all [installed,local]
tini/now 0.19.0-1 amd64 [installed,local]
tipa/now 2:1.3-21 all [installed,local]
tzdata/now 2025b-0ubuntu0.24.04.1 all [installed,local]
ubuntu-keyring/now 2023.11.28.1 all [installed,local]
ucf/now 3.0043+nmu1 all [installed,local]
unminimize/now 0.2.1 amd64 [installed,local]
unzip/now 6.0-28ubuntu4.1 amd64 [installed,local]
util-linux/now 2.39.3-9ubuntu6.3 amd64 [installed,local]
vim-common/now 2:9.1.0016-1ubuntu7.9 all [installed,local]
vim-tiny/now 2:9.1.0016-1ubuntu7.9 amd64 [installed,local]
wget/now 1.21.4-1ubuntu4.1 amd64 [installed,local]
x11-common/now 1:7.7+23ubuntu3 all [installed,local]
xclip/now 0.13-3 amd64 [installed,local]
xdg-utils/now 1.1.3-4.1ubuntu3 all [installed,local]
xfonts-encodings/now 1:1.0.5-0ubuntu2 all [installed,local]
xfonts-utils/now 1:7.7+6build3 amd64 [installed,local]
xkb-data/now 2.41-2ubuntu1.1 all [installed,local]
xz-utils/now 5.6.1+really5.4.5-1ubuntu0.2 amd64 [installed,local]
zlib1g/now 1:1.3.dfsg-3.1ubuntu2.1 amd64 [installed,local]
R --version:
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
R --silent -e 'installed.packages(.Library)[, c(1,3)]':
> installed.packages(.Library)[, c(1,3)]
Package Version
abind "abind" "1.4-8"
affy "affy" "1.84.0"
affyio "affyio" "1.76.0"
annotate "annotate" "1.84.0"
AnnotationDbi "AnnotationDbi" "1.68.0"
AnnotationFilter "AnnotationFilter" "1.30.0"
AnnotationHub "AnnotationHub" "3.14.0"
aod "aod" "1.3.3"
ape "ape" "5.8-1"
apeglm "apeglm" "1.28.0"
aplot "aplot" "0.2.9"
ashr "ashr" "2.2-63"
askpass "askpass" "1.2.1"
assertthat "assertthat" "0.2.1"
assorthead "assorthead" "1.0.0"
backports "backports" "1.5.0"
base "base" "4.4.3"
base64enc "base64enc" "0.1-3"
bbmle "bbmle" "1.0.25.1"
bdsmatrix "bdsmatrix" "1.3-7"
beachmat "beachmat" "2.22.0"
BH "BH" "1.87.0-1"
Biobase "Biobase" "2.66.0"
BiocFileCache "BiocFileCache" "2.14.0"
BiocGenerics "BiocGenerics" "0.52.0"
BiocIO "BiocIO" "1.16.0"
BiocManager "BiocManager" "1.30.27"
BiocParallel "BiocParallel" "1.40.0"
BiocSingular "BiocSingular" "1.22.0"
BiocVersion "BiocVersion" "3.20.0"
biomaRt "biomaRt" "2.62.0"
Biostrings "Biostrings" "2.74.0"
biovizBase "biovizBase" "1.54.0"
bit "bit" "4.6.0"
bit64 "bit64" "4.6.0-1"
bitops "bitops" "1.0-9"
blob "blob" "1.2.4"
boot "boot" "1.3-32"
brew "brew" "1.0-10"
brio "brio" "1.1.5"
broom "broom" "1.0.11"
broom.helpers "broom.helpers" "1.22.0"
BSgenome "BSgenome" "1.74.0"
bslib "bslib" "0.9.0"
cachem "cachem" "1.1.0"
callr "callr" "3.7.6"
car "car" "3.1-3"
carData "carData" "3.0-5"
cards "cards" "0.7.1"
caret "caret" "7.0-1"
caTools "caTools" "1.18.3"
cellranger "cellranger" "1.1.0"
checkmate "checkmate" "2.3.3"
circlize "circlize" "0.4.16"
class "class" "7.3-23"
cli "cli" "3.6.5"
clipr "clipr" "0.8.0"
clock "clock" "0.7.3"
clue "clue" "0.3-66"
cluster "cluster" "2.1.8.1"
clusterProfiler "clusterProfiler" "4.14.0"
coda "coda" "0.19-4.1"
codetools "codetools" "0.2-20"
collections "collections" "0.3.9"
colorspace "colorspace" "2.1-2"
commonmark "commonmark" "2.0.0"
compiler "compiler" "4.4.3"
ComplexHeatmap "ComplexHeatmap" "2.22.0"
conflicted "conflicted" "1.2.0"
conquer "conquer" "1.3.3"
corpcor "corpcor" "1.6.10"
corrplot "corrplot" "0.95"
cowplot "cowplot" "1.2.0"
cpp11 "cpp11" "0.5.2"
crayon "crayon" "1.5.3"
credentials "credentials" "2.0.3"
crosstalk "crosstalk" "1.2.2"
curl "curl" "7.0.0"
cyclocomp "cyclocomp" "1.1.1"
data.table "data.table" "1.17.8"
datasets "datasets" "4.4.3"
DBI "DBI" "1.2.3"
dbplyr "dbplyr" "2.5.1"
DelayedArray "DelayedArray" "0.32.0"
DelayedMatrixStats "DelayedMatrixStats" "1.28.0"
deldir "deldir" "2.0-4"
dendextend "dendextend" "1.19.1"
Deriv "Deriv" "4.2.0"
desc "desc" "1.4.3"
DESeq2 "DESeq2" "1.46.0"
devtools "devtools" "2.4.6"
diagram "diagram" "1.6.5"
dials "dials" "1.4.2"
DiceDesign "DiceDesign" "1.10"
dichromat "dichromat" "2.0-0.1"
diffobj "diffobj" "0.3.6"
digest "digest" "0.6.39"
doBy "doBy" "4.7.1"
doParallel "doParallel" "1.0.17"
DOSE "DOSE" "4.0.0"
downlit "downlit" "0.4.5"
dplyr "dplyr" "1.1.4"
dtplyr "dtplyr" "1.3.2"
e1071 "e1071" "1.7-16"
edgeR "edgeR" "4.4.0"
ellipsis "ellipsis" "0.3.2"
emdbook "emdbook" "1.3.14"
enrichplot "enrichplot" "1.26.1"
ensembldb "ensembldb" "2.30.0"
EnvStats "EnvStats" "3.1.0"
etrunct "etrunct" "0.1"
evaluate "evaluate" "1.0.5"
fANCOVA "fANCOVA" "0.6-1"
fansi "fansi" "1.0.7"
farver "farver" "2.1.2"
fastcluster "fastcluster" "1.3.0"
fastmap "fastmap" "1.2.0"
fastmatch "fastmatch" "1.1-6"
fgsea "fgsea" "1.32.2"
filelock "filelock" "1.0.3"
fontawesome "fontawesome" "0.5.3"
forcats "forcats" "1.0.1"
foreach "foreach" "1.5.2"
forecast "forecast" "8.24.0"
foreign "foreign" "0.8-90"
formatR "formatR" "1.14"
Formula "Formula" "1.2-5"
fracdiff "fracdiff" "1.5-3"
fs "fs" "1.6.6"
furrr "furrr" "0.3.1"
futile.logger "futile.logger" "1.4.3"
futile.options "futile.options" "1.0.1"
future "future" "1.68.0"
future.apply "future.apply" "1.20.0"
gargle "gargle" "1.6.0"
gbRd "gbRd" "0.4.12"
genefilter "genefilter" "1.88.0"
generics "generics" "0.1.4"
GenomeInfoDb "GenomeInfoDb" "1.42.0"
GenomeInfoDbData "GenomeInfoDbData" "1.2.13"
GenomicAlignments "GenomicAlignments" "1.42.0"
GenomicFeatures "GenomicFeatures" "1.58.0"
GenomicRanges "GenomicRanges" "1.58.0"
gert "gert" "2.2.0"
GetoptLong "GetoptLong" "1.1.0"
GGally "GGally" "2.4.0"
ggforce "ggforce" "0.5.0"
ggfun "ggfun" "0.2.0"
ggnewscale "ggnewscale" "0.5.2"
ggplot2 "ggplot2" "4.0.1"
ggplotify "ggplotify" "0.1.3"
ggpubr "ggpubr" "0.6.2"
ggraph "ggraph" "2.2.1"
ggrepel "ggrepel" "0.9.6"
ggsci "ggsci" "4.1.0"
ggsignif "ggsignif" "0.6.4"
ggstats "ggstats" "0.11.0"
ggtangle "ggtangle" "0.0.9"
ggtree "ggtree" "3.14.0"
ggvenn "ggvenn" "0.1.19"
gh "gh" "1.5.0"
gitcreds "gitcreds" "0.1.2"
glmGamPoi "glmGamPoi" "1.18.0"
GlobalOptions "GlobalOptions" "0.1.3"
globals "globals" "0.18.0"
glue "glue" "1.8.0"
GO.db "GO.db" "3.20.0"
googledrive "googledrive" "2.1.2"
googlesheets4 "googlesheets4" "1.1.2"
GOSemSim "GOSemSim" "2.32.0"
gower "gower" "1.0.1"
GPfit "GPfit" "1.0-9"
gplots "gplots" "3.3.0"
graph "graph" "1.84.0"
graphics "graphics" "4.4.3"
graphite "graphite" "1.52.0"
graphlayouts "graphlayouts" "1.2.2"
grDevices "grDevices" "4.4.3"
grid "grid" "4.4.3"
gridExtra "gridExtra" "2.3"
gridGraphics "gridGraphics" "0.5-1"
grImport "grImport" "0.9-7"
GSEABase "GSEABase" "1.68.0"
gson "gson" "0.1.0"
GSVA "GSVA" "2.0.0"
gtable "gtable" "0.3.6"
gtools "gtools" "3.9.5"
Gviz "Gviz" "1.50.0"
hardhat "hardhat" "1.4.2"
haven "haven" "2.5.5"
HDF5Array "HDF5Array" "1.34.0"
hexbin "hexbin" "1.28.5"
highr "highr" "0.11"
Hmisc "Hmisc" "5.2-4"
hms "hms" "1.1.4"
htmlTable "htmlTable" "2.4.3"
htmltools "htmltools" "0.5.9"
htmlwidgets "htmlwidgets" "1.6.4"
httpuv "httpuv" "1.6.16"
httr "httr" "1.4.7"
httr2 "httr2" "1.2.1"
ids "ids" "1.0.1"
igraph "igraph" "2.1.4"
infer "infer" "1.0.9"
ini "ini" "0.3.1"
InteractionSet "InteractionSet" "1.34.0"
interp "interp" "1.1-6"
invgamma "invgamma" "1.2"
ipred "ipred" "0.9-15"
IRanges "IRanges" "2.40.0"
IRdisplay "IRdisplay" "1.1"
IRkernel "IRkernel" "1.3.2"
irlba "irlba" "2.3.5.1"
isoband "isoband" "0.2.7"
iterators "iterators" "1.0.14"
janitor "janitor" "2.2.1"
jpeg "jpeg" "0.1-11"
jquerylib "jquerylib" "0.1.4"
jsonlite "jsonlite" "2.0.0"
KEGGREST "KEGGREST" "1.46.0"
KernSmooth "KernSmooth" "2.23-26"
knitr "knitr" "1.50"
labeling "labeling" "0.4.3"
labelled "labelled" "2.16.0"
lambda.r "lambda.r" "1.2.4"
languageserver "languageserver" "0.3.16"
later "later" "1.4.4"
lattice "lattice" "0.22-7"
latticeExtra "latticeExtra" "0.6-31"
lava "lava" "1.8.2"
lazyeval "lazyeval" "0.2.2"
lhs "lhs" "1.2.0"
lifecycle "lifecycle" "1.0.4"
limma "limma" "3.62.1"
lintr "lintr" "3.3.0-1"
listenv "listenv" "0.10.0"
lme4 "lme4" "1.1-38"
lmerTest "lmerTest" "3.1-3"
lmtest "lmtest" "0.9-40"
locfit "locfit" "1.5-9.12"
lubridate "lubridate" "1.9.4"
magick "magick" "2.9.0"
magrittr "magrittr" "2.0.4"
MASS "MASS" "7.3-65"
Matrix "Matrix" "1.7-4"
MatrixGenerics "MatrixGenerics" "1.18.0"
MatrixModels "MatrixModels" "0.5-4"
matrixStats "matrixStats" "1.5.0"
memoise "memoise" "2.0.1"
methods "methods" "4.4.3"
mgcv "mgcv" "1.9-4"
microbenchmark "microbenchmark" "1.5.0"
mime "mime" "0.13"
miniUI "miniUI" "0.1.2"
minqa "minqa" "1.2.8"
mixsqp "mixsqp" "0.3-54"
modeldata "modeldata" "1.5.1"
modelenv "modelenv" "0.2.0"
ModelMetrics "ModelMetrics" "1.2.2.2"
modelr "modelr" "0.1.11"
munsell "munsell" "0.5.1"
mvtnorm "mvtnorm" "1.3-3"
nlme "nlme" "3.1-168"
nloptr "nloptr" "2.2.1"
nnet "nnet" "7.3-20"
nortest "nortest" "1.0-4"
numDeriv "numDeriv" "2016.8-1.1"
nycflights13 "nycflights13" "1.0.2"
openssl "openssl" "2.3.4"
openxlsx "openxlsx" "4.2.8.1"
openxlsx2 "openxlsx2" "1.21"
org.Hs.eg.db "org.Hs.eg.db" "3.20.0"
org.Mm.eg.db "org.Mm.eg.db" "3.20.0"
otel "otel" "0.2.0"
paletteer "paletteer" "1.6.0"
parallel "parallel" "4.4.3"
parallelDist "parallelDist" "0.2.7"
parallelly "parallelly" "1.45.1"
parsnip "parsnip" "1.4.0"
patchwork "patchwork" "1.3.2"
pbdZMQ "pbdZMQ" "0.3-14"
pbkrtest "pbkrtest" "0.5.5"
pheatmap "pheatmap" "1.0.13"
pillar "pillar" "1.11.1"
pkgbuild "pkgbuild" "1.4.8"
pkgconfig "pkgconfig" "2.0.3"
pkgdown "pkgdown" "2.2.0"
pkgload "pkgload" "1.4.1"
plogr "plogr" "0.2.0"
plotly "plotly" "4.11.0"
plyr "plyr" "1.8.9"
png "png" "0.1-8"
polyclip "polyclip" "1.10-7"
polynom "polynom" "1.4-1"
praise "praise" "1.0.0"
preprocessCore "preprocessCore" "1.68.0"
prettyunits "prettyunits" "1.2.0"
prismatic "prismatic" "1.1.2"
pROC "pROC" "1.19.0.1"
processx "processx" "3.8.6"
prodlim "prodlim" "2025.04.28"
profvis "profvis" "0.4.0"
progress "progress" "1.2.3"
progressr "progressr" "0.18.0"
promises "promises" "1.5.0"
ProtGenerics "ProtGenerics" "1.38.0"
proxy "proxy" "0.4-27"
ps "ps" "1.9.1"
purrr "purrr" "1.2.0"
quadprog "quadprog" "1.5-8"
quantmod "quantmod" "0.4.28"
quantreg "quantreg" "6.1"
qvalue "qvalue" "2.38.0"
R.cache "R.cache" "0.17.0"
R.methodsS3 "R.methodsS3" "1.8.2"
R.oo "R.oo" "1.27.1"
R.utils "R.utils" "2.13.0"
R6 "R6" "2.6.1"
ragg "ragg" "1.5.0"
randomForest "randomForest" "4.7-1.2"
rappdirs "rappdirs" "0.3.3"
rbibutils "rbibutils" "2.4"
rcmdcheck "rcmdcheck" "1.4.0"
RColorBrewer "RColorBrewer" "1.1-3"
Rcpp "Rcpp" "1.1.0"
RcppArmadillo "RcppArmadillo" "15.2.2-1"
RcppEigen "RcppEigen" "0.3.4.0.2"
RcppNumerical "RcppNumerical" "0.6-0"
RcppParallel "RcppParallel" "5.1.11-1"
RCurl "RCurl" "1.98-1.17"
Rdpack "Rdpack" "2.6.4"
reactome.db "reactome.db" "1.89.0"
ReactomePA "ReactomePA" "1.50.0"
readr "readr" "2.1.6"
readxl "readxl" "1.4.5"
recipes "recipes" "1.3.1"
reformulas "reformulas" "0.4.2"
remaCor "remaCor" "0.0.20"
rematch "rematch" "2.0.0"
rematch2 "rematch2" "2.1.2"
remotes "remotes" "2.5.0"
repr "repr" "1.1.7"
reprex "reprex" "2.1.1"
reshape2 "reshape2" "1.4.5"
restfulr "restfulr" "0.0.16"
rex "rex" "1.2.1"
rhdf5 "rhdf5" "2.50.0"
rhdf5filters "rhdf5filters" "1.18.0"
Rhdf5lib "Rhdf5lib" "1.28.0"
RhpcBLASctl "RhpcBLASctl" "0.23-42"
Rhtslib "Rhtslib" "3.2.0"
rjson "rjson" "0.2.23"
rlang "rlang" "1.1.6"
rmarkdown "rmarkdown" "2.30"
RobustRankAggreg "RobustRankAggreg" "1.2.1"
RODBC "RODBC" "1.3-26"
roxygen2 "roxygen2" "7.3.3"
rpart "rpart" "4.1.24"
rprojroot "rprojroot" "2.1.1"
rsample "rsample" "1.3.1"
Rsamtools "Rsamtools" "2.22.0"
RSQLite "RSQLite" "2.4.5"
rstatix "rstatix" "0.7.3"
rstudioapi "rstudioapi" "0.17.1"
rsvd "rsvd" "1.0.5"
rtracklayer "rtracklayer" "1.66.0"
rversions "rversions" "3.0.0"
rvest "rvest" "1.0.5"
S4Arrays "S4Arrays" "1.6.0"
S4Vectors "S4Vectors" "0.44.0"
S7 "S7" "0.2.1"
sass "sass" "0.4.10"
ScaledMatrix "ScaledMatrix" "1.14.0"
scales "scales" "1.4.0"
scatterpie "scatterpie" "0.2.6"
scuttle "scuttle" "1.16.0"
selectr "selectr" "0.5-0"
sessioninfo "sessioninfo" "1.2.3"
sfd "sfd" "0.1.0"
shape "shape" "1.4.6.1"
shiny "shiny" "1.12.0"
SingleCellExperiment "SingleCellExperiment" "1.28.0"
slider "slider" "0.3.3"
snakecase "snakecase" "0.11.1"
snow "snow" "0.4-4"
sourcetools "sourcetools" "0.1.7-1"
SparseArray "SparseArray" "1.6.0"
SparseM "SparseM" "1.84-2"
sparseMatrixStats "sparseMatrixStats" "1.18.0"
sparsevctrs "sparsevctrs" "0.3.4"
SpatialExperiment "SpatialExperiment" "1.16.0"
splines "splines" "4.4.3"
SQUAREM "SQUAREM" "2021.1"
statmod "statmod" "1.5.1"
stats "stats" "4.4.3"
stats4 "stats4" "4.4.3"
strawr "strawr" "0.0.92"
stringi "stringi" "1.8.7"
stringr "stringr" "1.6.0"
styler "styler" "1.11.0"
SummarizedExperiment "SummarizedExperiment" "1.36.0"
survival "survival" "3.8-3"
sva "sva" "3.54.0"
svglite "svglite" "2.2.2"
sys "sys" "3.4.3"
systemfonts "systemfonts" "1.3.1"
tailor "tailor" "0.1.0"
tcltk "tcltk" "4.4.3"
testthat "testthat" "3.3.1"
textshaping "textshaping" "1.0.4"
tibble "tibble" "3.3.0"
tidygraph "tidygraph" "1.3.0"
tidymodels "tidymodels" "1.4.1"
tidyr "tidyr" "1.3.1"
tidyselect "tidyselect" "1.2.1"
tidytree "tidytree" "0.4.6"
tidyverse "tidyverse" "2.0.0"
timechange "timechange" "0.3.0"
timeDate "timeDate" "4051.111"
tinytex "tinytex" "0.58"
tools "tools" "4.4.3"
trackViewer "trackViewer" "1.42.0"
treeio "treeio" "1.30.0"
truncnorm "truncnorm" "1.0-9"
tseries "tseries" "0.10-58"
TTR "TTR" "0.24.4"
tune "tune" "2.0.1"
tweenr "tweenr" "2.0.3"
txdbmaker "txdbmaker" "1.2.0"
tximeta "tximeta" "1.24.0"
tximport "tximport" "1.34.0"
tzdb "tzdb" "0.5.0"
UCSC.utils "UCSC.utils" "1.2.0"
urca "urca" "1.3-4"
urlchecker "urlchecker" "1.0.1"
usethis "usethis" "3.2.1"
utf8 "utf8" "1.2.6"
utils "utils" "4.4.3"
uuid "uuid" "1.2-1"
variancePartition "variancePartition" "1.36.2"
VariantAnnotation "VariantAnnotation" "1.52.0"
vctrs "vctrs" "0.6.5"
viridis "viridis" "0.6.5"
viridisLite "viridisLite" "0.4.2"
vroom "vroom" "1.6.7"
vsn "vsn" "3.74.0"
waldo "waldo" "0.6.2"
warp "warp" "0.2.2"
whisker "whisker" "0.4.1"
withr "withr" "3.0.2"
workflows "workflows" "1.3.0"
workflowsets "workflowsets" "1.1.1"
writexl "writexl" "1.5.4"
xfun "xfun" "0.54"
XML "XML" "3.99-0.20"
xml2 "xml2" "1.5.0"
xmlparsedata "xmlparsedata" "1.0.5"
xopen "xopen" "1.0.1"
xtable "xtable" "1.8-4"
xts "xts" "0.14.1"
XVector "XVector" "0.46.0"
yaml "yaml" "2.3.11"
yardstick "yardstick" "1.3.2"
yulab.utils "yulab.utils" "0.2.2"
zip "zip" "2.3.3"
zlibbioc "zlibbioc" "1.52.0"
zoo "zoo" "1.8-14"
>
>
julia -E 'using InteractiveUtils; versioninfo()':
Julia Version 1.12.2
Commit ca9b6662be4 (2025-11-20 16:25 UTC)
Build Info:
Official https://julialang.org release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 × AMD EPYC 7763 64-Core Processor
WORD_SIZE: 64
LLVM: libLLVM-18.1.7 (ORCJIT, znver3)
GC: Built with stock GC
Threads: 1 default, 1 interactive, 1 GC (on 4 virtual cores)
Environment:
JULIA_DEPOT_PATH = /opt/julia
JULIA_PKGDIR = /opt/julia
nothing
julia -E 'import Pkg; Pkg.status()':
Status `/opt/julia/environments/v1.12/Project.toml`
[f67ccb44] HDF5 v0.17.2
[7073ff75] IJulia v1.33.0
[c3e4b0f8] Pluto v0.20.21
nothing