x86_64 default rnaseq notebook f9955b2299c9 - huchlab/sequencing-docker-stacks GitHub Wiki
- Build timestamp: 2025-08-06T10:44:30Z
- Docker image:
quay.io/huchlab/rnaseq-notebook:f9955b2299c9 - Docker image size: 10.7GB
- Git commit SHA: f9955b2299c9293c6c9efd07af1f5223793c47b4
- Git commit message:
Merge pull request #108 from huchlab/fbnrst/issue71
use github access token for devtools:install_github
Python 3.12.11
conda info:
active environment : None
user config file : /home/jovyan/.condarc
populated config files : /opt/conda/.condarc
/home/jovyan/.condarc
conda version : 25.5.1
conda-build version : not installed
python version : 3.12.11.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen2
__conda=25.5.1=0
__glibc=2.39=0
__linux=6.11.0=0
__unix=0=0
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
user-agent : conda/25.5.1 requests/2.32.4 CPython/3.12.11 Linux/6.11.0-1018-azure ubuntu/24.04.2 glibc/2.39 solver/libmamba conda-libmamba-solver/25.4.0 libmambapy/2.3.1
UID:GID : 1000:100
netrc file : None
offline mode : False
mamba info:
libmamba version : 2.3.1
mamba version : 2.3.1
curl version : libcurl/8.14.1 OpenSSL/3.5.1 zlib/1.3.1 zstd/1.5.7 libssh2/1.11.1 nghttp2/1.64.0
libarchive version : libarchive 3.8.1 zlib/1.3.1 liblzma/5.8.1 bz2lib/1.0.8 liblz4/1.10.0 libzstd/1.5.7 liblzo2/2.10 openssl/3.5.0 libb2/bundled
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
__linux=6.11.0=0
__glibc=2.39=0
__archspec=1=x86_64_v3
channels : 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
base environment : /opt/conda
platform : linux-64
mamba list:
List of packages in environment: "/opt/conda"
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────────────────
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arrow 1.3.0 pyhd8ed1ab_1 conda-forge
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bioconductor-rhdf5 2.50.0 r44h77050f0_1 bioconda
bioconductor-rhdf5filters 1.18.0 r44h77050f0_1 bioconda
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bioconductor-rhtslib 3.2.0 r44h15a9599_2 bioconda
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bioconductor-treeio 1.30.0 r44hdfd78af_0 bioconda
bioconductor-txdbmaker 1.2.0 r44hdfd78af_0 bioconda
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bioconductor-tximport 1.34.0 r44hdfd78af_0 bioconda
bioconductor-ucsc.utils 1.2.0 r44h9ee0642_1 bioconda
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bioconductor-xvector 0.46.0 r44h15a9599_2 bioconda
bioconductor-zlibbioc 1.52.0 r44h3df3fcb_2 bioconda
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decorator 5.2.1 pyhd8ed1ab_0 conda-forge
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dill 0.4.0 pyhd8ed1ab_0 conda-forge
distributed 2025.7.0 pyhe01879c_0 conda-forge
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fmt 11.2.0 h07f6e7f_0 conda-forge
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fsspec 2025.7.0 pyhd8ed1ab_0 conda-forge
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gcc_impl_linux-64 15.1.0 h4393ad2_4 conda-forge
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r-lmertest 3.1_3 r44hc72bb7e_3 conda-forge
r-lmtest 0.9_40 r44hbcb9c34_3 conda-forge
r-locfit 1.5_9.12 r44h2b5f3a1_0 conda-forge
r-lubridate 1.9.4 r44h2b5f3a1_0 conda-forge
r-magick 2.8.6 r44h93ab643_0 conda-forge
r-magrittr 2.0.3 r44hb1dbf0f_3 conda-forge
r-mapproj 1.2.12 r44h2b5f3a1_0 conda-forge
r-maps 3.4.3 r44h2b5f3a1_0 conda-forge
r-mass 7.3_64 r44h2b5f3a1_0 conda-forge
r-matrix 1.7_3 r44h2ae2be5_0 conda-forge
r-matrixmodels 0.5_4 r44hc72bb7e_0 conda-forge
r-matrixstats 1.5.0 r44h2b5f3a1_0 conda-forge
r-memoise 2.0.1 r44hc72bb7e_3 conda-forge
r-mgcv 1.9_3 r44h2ae2be5_0 conda-forge
r-microbenchmark 1.5.0 r44h2b5f3a1_0 conda-forge
r-mime 0.13 r44h2b5f3a1_0 conda-forge
r-miniui 0.1.2 r44hc72bb7e_0 conda-forge
r-minqa 1.2.8 r44ha936806_0 conda-forge
r-mixsqp 0.3_54 r44hb79369c_3 conda-forge
r-modeldata 1.5.0 r44hc72bb7e_0 conda-forge
r-modelenv 0.2.0 r44hc72bb7e_0 conda-forge
r-modelmetrics 1.2.2.2 r44h0d4f4ea_4 conda-forge
r-modelr 0.1.11 r44hc72bb7e_2 conda-forge
r-munsell 0.5.1 r44hc72bb7e_1 conda-forge
r-mvtnorm 1.3_3 r44h9ad1c49_0 conda-forge
r-nlme 3.1_168 r44hb67ce94_0 conda-forge
r-nloptr 2.2.1 r44hb8c4c88_0 conda-forge
r-nnet 7.3_20 r44h2b5f3a1_0 conda-forge
r-nortest 1.0_4 r44hc72bb7e_1006 conda-forge
r-numderiv 2016.8_1.1 r44hc72bb7e_6 conda-forge
r-nycflights13 1.0.2 r44h785f33e_4 conda-forge
r-oompabase 3.2.10 r44hc72bb7e_0 conda-forge
r-openssl 2.3.3 r44he8289e2_0 conda-forge
r-paletteer 1.6.0 r44hc72bb7e_1 conda-forge
r-palr 0.4.0 r44hc72bb7e_1 conda-forge
r-pals 1.10 r44hc72bb7e_0 conda-forge
r-paralleldist 0.2.6 r44hb79369c_3 conda-forge
r-parallelly 1.45.1 r44h54b55ab_0 conda-forge
r-parsnip 1.3.2 r44hc72bb7e_0 conda-forge
r-patchwork 1.3.1 r44hc72bb7e_0 conda-forge
r-pbdzmq 0.3_14 r44h549f438_0 conda-forge
r-pbkrtest 0.5.5 r44hc72bb7e_0 conda-forge
r-pheatmap 1.0.13 r44hc72bb7e_0 conda-forge
r-pillar 1.11.0 r44hc72bb7e_0 conda-forge
r-pkgbuild 1.4.8 r44hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r44hc72bb7e_4 conda-forge
r-pkgdown 2.1.3 r44hc72bb7e_0 conda-forge
r-pkgload 1.4.0 r44hc72bb7e_0 conda-forge
r-plogr 0.2.0 r44hc72bb7e_1006 conda-forge
r-plotly 4.11.0 r44hc72bb7e_0 conda-forge
r-plyr 1.8.9 r44h3697838_2 conda-forge
r-png 0.1_8 r44h21f035c_2 conda-forge
r-polyclip 1.10_7 r44h0d4f4ea_0 conda-forge
r-polynom 1.4_1 r44hc72bb7e_3 conda-forge
r-praise 1.0.0 r44hc72bb7e_1008 conda-forge
r-prettyunits 1.2.0 r44hc72bb7e_1 conda-forge
r-prismatic 1.1.2 r44hc72bb7e_1 conda-forge
r-proc 1.19.0.1 r44h3697838_0 conda-forge
r-processx 3.8.6 r44h2b5f3a1_0 conda-forge
r-prodlim 2025.04.28 r44h93ab643_0 conda-forge
r-profvis 0.4.0 r44h2b5f3a1_0 conda-forge
r-progress 1.2.3 r44hc72bb7e_1 conda-forge
r-progressr 0.15.1 r44hc72bb7e_0 conda-forge
r-promises 1.3.2 r44h93ab643_0 conda-forge
r-proxy 0.4_27 r44hb1dbf0f_3 conda-forge
r-ps 1.9.1 r44h2b5f3a1_0 conda-forge
r-purrr 1.1.0 r44h54b55ab_0 conda-forge
r-quadprog 1.5_8 r44hc2011d3_6 conda-forge
r-quantmod 0.4.28 r44hc72bb7e_0 conda-forge
r-quantreg 6.00 r44h012206f_0 conda-forge
r-r.cache 0.17.0 r44hc72bb7e_0 conda-forge
r-r.methodss3 1.8.2 r44hc72bb7e_3 conda-forge
r-r.oo 1.27.1 r44hc72bb7e_0 conda-forge
r-r.utils 2.13.0 r44hc72bb7e_0 conda-forge
r-r6 2.6.1 r44hc72bb7e_0 conda-forge
r-ragg 1.4.0 r44hdcc764c_0 conda-forge
r-randomforest 4.7_1.2 r44hb67ce94_0 conda-forge
r-rappdirs 0.3.3 r44hb1dbf0f_3 conda-forge
r-rbibutils 2.3 r44h2b5f3a1_0 conda-forge
r-rcmdcheck 1.4.0 r44h785f33e_3 conda-forge
r-rcolorbrewer 1.1_3 r44h785f33e_3 conda-forge
r-rcpp 1.1.0 r44h93ab643_0 conda-forge
r-rcpparmadillo 14.6.0_1 r44h3704496_0 conda-forge
r-rcppeigen 0.3.4.0.2 r44hb79369c_0 conda-forge
r-rcppnumerical 0.6_0 r44h0d4f4ea_1 conda-forge
r-rcppparallel 5.1.9 r44h93ab643_1 conda-forge
r-rcurl 1.98_1.16 r44he8228da_1 conda-forge
r-rdpack 2.6.4 r44hc72bb7e_0 conda-forge
r-readr 2.1.5 r44h0d4f4ea_1 conda-forge
r-readxl 1.4.5 r44h328fee5_0 conda-forge
r-recipes 1.3.1 r44hc72bb7e_0 conda-forge
r-reformulas 0.4.1 r44hc72bb7e_0 conda-forge
r-remacor 0.0.18 r44hc2d650c_2 conda-forge
r-rematch 2.0.0 r44hc72bb7e_1 conda-forge
r-rematch2 2.1.2 r44hc72bb7e_4 conda-forge
r-remotes 2.5.0 r44hc72bb7e_1 conda-forge
r-repr 1.1.7 r44h785f33e_1 conda-forge
r-reprex 2.1.1 r44hc72bb7e_1 conda-forge
r-reshape2 1.4.4 r44h0d4f4ea_4 conda-forge
r-restfulr 0.0.16 r44h5ef9028_0 bioconda
r-rex 1.2.1 r44hc72bb7e_3 conda-forge
r-rgl 1.3.24 r44he96d32b_0 conda-forge
r-rhpcblasctl 0.23_42 r44hb1dbf0f_2 conda-forge
r-rjson 0.2.23 r44h93ab643_0 conda-forge
r-rlang 1.1.6 r44h93ab643_0 conda-forge
r-rmarkdown 2.29 r44hc72bb7e_0 conda-forge
r-robustrankaggreg 1.2.1 r44hc72bb7e_3 conda-forge
r-rodbc 1.3_26 r44h54b55ab_0 conda-forge
r-roxygen2 7.3.2 r44h0d4f4ea_1 conda-forge
r-rpart 4.1.24 r44h2b5f3a1_0 conda-forge
r-rprojroot 2.1.0 r44hc72bb7e_0 conda-forge
r-rsample 1.3.1 r44hc72bb7e_0 conda-forge
r-rsqlite 2.4.2 r44h3697838_0 conda-forge
r-rstatix 0.7.2 r44hc72bb7e_2 conda-forge
r-rstudioapi 0.17.1 r44hc72bb7e_0 conda-forge
r-rsvd 1.0.5 r44hc72bb7e_3 conda-forge
r-rversions 2.1.2 r44hc72bb7e_3 conda-forge
r-rvest 1.0.4 r44hc72bb7e_1 conda-forge
r-s7 0.2.0 r44h54b55ab_0 conda-forge
r-sass 0.4.10 r44h93ab643_0 conda-forge
r-scales 1.4.0 r44hc72bb7e_0 conda-forge
r-scatterpie 0.2.5 r44hc72bb7e_0 conda-forge
r-scico 1.5.0 r44hc72bb7e_1 conda-forge
r-selectr 0.4_2 r44hc72bb7e_4 conda-forge
r-sessioninfo 1.2.3 r44hc72bb7e_0 conda-forge
r-sfd 0.1.0 r44hc72bb7e_1 conda-forge
r-shape 1.4.6.1 r44ha770c72_1 conda-forge
r-shiny 1.11.1 r44h785f33e_0 conda-forge
r-slider 0.3.2 r44h93ab643_0 conda-forge
r-snow 0.4_4 r44hc72bb7e_3 conda-forge
r-sourcetools 0.1.7_1 r44ha18555a_2 conda-forge
r-sparsem 1.84_2 r44hc4980d5_0 conda-forge
r-sparsevctrs 0.3.4 r44h2b5f3a1_0 conda-forge
r-squarem 2021.1 r44hc72bb7e_3 conda-forge
r-statmod 1.5.0 r44ha36c22a_2 conda-forge
r-stringi 1.8.7 r44h3c328a7_0 conda-forge
r-stringr 1.5.1 r44h785f33e_1 conda-forge
r-styler 1.10.3 r44hc72bb7e_1 conda-forge
r-survival 3.8_3 r44h2b5f3a1_0 conda-forge
r-sys 3.4.3 r44h2b5f3a1_0 conda-forge
r-systemfonts 1.2.3 r44h5c043a3_0 conda-forge
r-testthat 3.2.3 r44h3697838_1 conda-forge
r-textshaping 1.0.1 r44h16f7c1a_0 conda-forge
r-tibble 3.3.0 r44h2b5f3a1_0 conda-forge
r-tidygraph 1.3.0 r44h0d4f4ea_1 conda-forge
r-tidymodels 1.3.0 r44hc72bb7e_0 conda-forge
r-tidyr 1.3.1 r44h0d4f4ea_1 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_1 conda-forge
r-tidytree 0.4.6 r44hc72bb7e_1 conda-forge
r-tidyverse 2.0.0 r44h785f33e_2 conda-forge
r-timechange 0.3.0 r44ha18555a_1 conda-forge
r-timedate 4041.110 r44hc72bb7e_0 conda-forge
r-tinytex 0.57 r44hc72bb7e_0 conda-forge
r-truncnorm 1.0_9 r44h2b5f3a1_4 conda-forge
r-tseries 0.10_58 r44h8461fee_0 conda-forge
r-ttr 0.24.4 r44hdb488b9_1 conda-forge
r-tune 1.3.0 r44hc72bb7e_1 conda-forge
r-tweenr 2.0.3 r44h0d4f4ea_1 conda-forge
r-tzdb 0.5.0 r44h93ab643_0 conda-forge
r-urca 1.3_4 r44hbcb9c34_1 conda-forge
r-urlchecker 1.0.1 r44hc72bb7e_3 conda-forge
r-usethis 3.1.0 r44hc72bb7e_0 conda-forge
r-utf8 1.2.6 r44h2b5f3a1_0 conda-forge
r-uuid 1.2_1 r44hdb488b9_0 conda-forge
r-vctrs 0.6.5 r44h0d4f4ea_1 conda-forge
r-viridis 0.6.5 r44hc72bb7e_1 conda-forge
r-viridislite 0.4.2 r44hc72bb7e_2 conda-forge
r-vroom 1.6.5 r44h0d4f4ea_1 conda-forge
r-waldo 0.6.2 r44hc72bb7e_0 conda-forge
r-warp 0.2.1 r44hb1dbf0f_1 conda-forge
r-whisker 0.4.1 r44hc72bb7e_2 conda-forge
r-withr 3.0.2 r44hc72bb7e_0 conda-forge
r-workflows 1.2.0 r44hc72bb7e_0 conda-forge
r-workflowsets 1.1.1 r44h785f33e_0 conda-forge
r-writexl 1.5.4 r44he23165d_0 conda-forge
r-xfun 0.52 r44h93ab643_0 conda-forge
r-xml 3.99_0.17 r44h5bae778_2 conda-forge
r-xml2 1.3.8 r44h1bb2df6_0 conda-forge
r-xmlparsedata 1.0.5 r44hc72bb7e_3 conda-forge
r-xopen 1.0.1 r44hc72bb7e_1 conda-forge
r-xtable 1.8_4 r44hc72bb7e_6 conda-forge
r-xts 0.14.1 r44h2b5f3a1_0 conda-forge
r-yaml 2.3.10 r44hdb488b9_0 conda-forge
r-yardstick 1.3.2 r44h2b5f3a1_0 conda-forge
r-yulab.utils 0.2.0 r44hc72bb7e_0 conda-forge
r-zip 2.3.3 r44h2b5f3a1_0 conda-forge
r-zoo 1.8_14 r44h2b5f3a1_0 conda-forge
rav1e 0.7.1 h8fae777_3 conda-forge
re2 2025.07.22 h5a314c3_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
reproc 14.2.5.post0 hb9d3cd8_0 conda-forge
reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge
requests 2.32.4 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 0.26.0 py312h680f630_0 conda-forge
rpy2 3.6.2 py312r44h4bada26_0 conda-forge
ruamel.yaml 0.18.14 py312h66e93f0_0 conda-forge
ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge
s2n 1.5.23 h8e187f5_0 conda-forge
scikit-image 0.25.2 py312hf9745cd_1 conda-forge
scikit-learn 1.7.1 py312h4f0b9e3_0 conda-forge
scipy 1.16.0 py312hf734454_0 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
setuptools 80.9.0 pyhff2d567_0 conda-forge
simdjson 3.13.0 h84d6215_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_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_1 conda-forge
soupsieve 2.7 pyhd8ed1ab_0 conda-forge
sqlalchemy 2.0.42 py312h4c3975b_0 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.5 py312h8b63200_0 conda-forge
stdlib-list 0.11.1 pyhd8ed1ab_0 conda-forge
svt-av1 3.0.2 h5888daf_0 conda-forge
sympy 1.14.0 pyh2585a3b_105 conda-forge
sysroot_linux-64 2.34 h087de78_2 conda-forge
tblib 3.1.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tifffile 2025.6.11 pyhd8ed1ab_0 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tktable 2.10 h8d826fa_7 conda-forge
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomli 2.2.1 pyhe01879c_2 conda-forge
tomlkit 0.13.3 pyha770c72_0 conda-forge
toolz 1.0.0 pyhd8ed1ab_1 conda-forge
tornado 6.5.1 py312h66e93f0_0 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
types-python-dateutil 2.9.0.20250708 pyhd8ed1ab_0 conda-forge
typing-extensions 4.14.1 h4440ef1_0 conda-forge
typing-inspection 0.4.1 pyhd8ed1ab_0 conda-forge
typing_extensions 4.14.1 pyhe01879c_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
tzlocal 5.3 py312h7900ff3_0 conda-forge
unicodedata2 16.0.0 py312h66e93f0_0 conda-forge
unixodbc 2.3.12 h661eb56_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
wayland 1.24.0 h3e06ad9_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.14 pyhd8ed1ab_0 conda-forge
x265 3.5 h924138e_3 conda-forge
xkeyboard-config 2.45 hb9d3cd8_0 conda-forge
xlrd 2.0.1 pyhd8ed1ab_3 conda-forge
xmltodict 0.14.2 pyhd8ed1ab_1 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 hb9d3cd8_0 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 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_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
xyzservices 2025.4.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yaml-cpp 0.8.0 h3f2d84a_0 conda-forge
yarl 1.20.1 py312h178313f_0 conda-forge
yq 3.4.3 pyhe01879c_2 conda-forge
zeromq 4.3.5 h3b0a872_7 conda-forge
zfp 1.0.1 h5888daf_2 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.2.4 h7955e40_0 conda-forge
zstandard 0.23.0 py312h66e93f0_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 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 13ubuntu10.2 amd64 [installed,local]
base-passwd/now 3.6.3build1 amd64 [installed,local]
bash/now 5.2.21-2ubuntu4 amd64 [installed,local]
binutils-common/now 2.42-4ubuntu2.5 amd64 [installed,local]
binutils-x86-64-linux-gnu/now 2.42-4ubuntu2.5 amd64 [installed,local]
binutils/now 2.42-4ubuntu2.5 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 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 1.22.6ubuntu6.1 all [installed,local]
dpkg/now 1.22.6ubuntu6.1 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]
fonts-liberation/now 1:2.1.5-3 all [installed,local]
fonts-lmodern/now 2.005-1 all [installed,local]
fonts-urw-base35/now 20200910-8 all [installed,local]
g++-13-x86-64-linux-gnu/now 13.3.0-6ubuntu2~24.04 amd64 [installed,local]
g++-13/now 13.3.0-6ubuntu2~24.04 amd64 [installed,local]
g++-x86-64-linux-gnu/now 4:13.2.0-7ubuntu1 amd64 [installed,local]
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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-dri2-0/now 1.15-1ubuntu2 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-1.3ubuntu3.3 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 6.8.0-71.71 amd64 [installed,local]
locales/now 2.39-0ubuntu8.5 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 24.2.8-1ubuntu1~24.04.1 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 1:9.6p1-3ubuntu13.13 amd64 [installed,local]
openssl/now 3.0.13-0ubuntu3.5 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 amd64 [installed,local]
python3.12-minimal/now 3.12.3-1ubuntu0.7 amd64 [installed,local]
python3.12/now 3.12.3-1ubuntu0.7 amd64 [installed,local]
python3/now 3.12.3-0ubuntu2 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 2:9.1.0016-1ubuntu7.8 all [installed,local]
vim-tiny/now 2:9.1.0016-1ubuntu7.8 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" "1.4-5"
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" "0.2.8"
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" "1.30.26"
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" "1.3-31"
brew "brew" "1.0-10"
brio "brio" "1.1.5"
broom "broom" "1.0.9"
broom.helpers "broom.helpers" "1.21.0"
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" "0.6.1"
caret "caret" "6.0-94"
caTools "caTools" "1.18.3"
cellranger "cellranger" "1.1.0"
checkmate "checkmate" "2.3.2"
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" "0.3.8"
colorspace "colorspace" "2.1-1"
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" "2.0.2"
crosstalk "crosstalk" "1.2.1"
curl "curl" "6.4.0"
cyclocomp "cyclocomp" "1.1.1"
data.table "data.table" "1.17.8"
datasets "datasets" "4.4.3"
DBI "DBI" "1.2.3"
dbplyr "dbplyr" "2.5.0"
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" "2.4.5"
diagram "diagram" "1.6.5"
dials "dials" "1.4.1"
DiceDesign "DiceDesign" "1.10"
dichromat "dichromat" "2.0-0.1"
diffobj "diffobj" "0.3.6"
digest "digest" "0.6.37"
doBy "doBy" "4.7.0"
doFuture "doFuture" "1.1.2"
doParallel "doParallel" "1.0.17"
DOSE "DOSE" "4.0.0"
downlit "downlit" "0.4.4"
dplyr "dplyr" "1.1.4"
dtplyr "dtplyr" "1.3.1"
e1071 "e1071" "1.7-16"
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" "1.0.4"
fANCOVA "fANCOVA" "0.6-1"
fansi "fansi" "1.0.6"
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" "1.0.0"
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" "1.67.0"
future.apply "future.apply" "1.20.0"
gameofthrones "gameofthrones" "1.0.2"
gargle "gargle" "1.5.2"
gbRd "gbRd" "0.4.12"
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" "2.1.4"
GetoptLong "GetoptLong" "1.0.5"
GGally "GGally" "2.3.0"
ggforce "ggforce" "0.5.0"
ggfun "ggfun" "0.2.0"
ggnewscale "ggnewscale" "0.5.2"
ggplot2 "ggplot2" "3.5.2"
ggplotify "ggplotify" "0.1.2"
ggpubr "ggpubr" "0.6.1"
ggraph "ggraph" "2.2.1"
ggrepel "ggrepel" "0.9.6"
ggsci "ggsci" "3.2.0"
ggsignif "ggsignif" "0.6.4"
ggstats "ggstats" "0.10.0"
ggtangle "ggtangle" "0.0.7"
ggthemes "ggthemes" "5.1.0"
ggtree "ggtree" "3.14.0"
gh "gh" "1.5.0"
gitcreds "gitcreds" "0.1.2"
glmGamPoi "glmGamPoi" "1.18.0"
GlobalOptions "GlobalOptions" "0.1.2"
globals "globals" "0.18.0"
glue "glue" "1.8.0"
GO.db "GO.db" "3.20.0"
googledrive "googledrive" "2.1.1"
googlesheets4 "googlesheets4" "1.1.1"
GOSemSim "GOSemSim" "2.32.0"
gower "gower" "1.0.1"
GPfit "GPfit" "1.0-9"
gplots "gplots" "3.2.0"
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"
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" "1.4.1"
harrypotter "harrypotter" "2.1.1"
haven "haven" "2.5.4"
HDF5Array "HDF5Array" "1.34.0"
hexbin "hexbin" "1.28.5"
highr "highr" "0.11"
Hmisc "Hmisc" "5.2-3"
hms "hms" "1.1.3"
htmlTable "htmlTable" "2.4.3"
htmltools "htmltools" "0.5.8.1"
htmlwidgets "htmlwidgets" "1.6.4"
httpuv "httpuv" "1.6.15"
httr "httr" "1.4.7"
httr2 "httr2" "1.2.1"
ids "ids" "1.0.1"
igraph "igraph" "2.0.3"
infer "infer" "1.0.9"
ini "ini" "0.3.1"
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"
jcolors "jcolors" "0.0.5"
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" "2.14.1"
lambda.r "lambda.r" "1.2.4"
languageserver "languageserver" "0.3.16"
later "later" "1.4.2"
lattice "lattice" "0.22-7"
latticeExtra "latticeExtra" "0.6-30"
lava "lava" "1.8.1"
lazyeval "lazyeval" "0.2.2"
lhs "lhs" "1.2.0"
lifecycle "lifecycle" "1.0.4"
limma "limma" "3.62.1"
lintr "lintr" "3.2.0"
listenv "listenv" "0.9.1"
lme4 "lme4" "1.1-37"
lmerTest "lmerTest" "3.1-3"
lmtest "lmtest" "0.9-40"
locfit "locfit" "1.5-9.12"
lubridate "lubridate" "1.9.4"
magick "magick" "2.8.6"
magrittr "magrittr" "2.0.3"
mapproj "mapproj" "1.2.12"
maps "maps" "3.4.3"
MASS "MASS" "7.3-64"
Matrix "Matrix" "1.7-3"
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" "1.9-3"
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" "1.5.0"
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"
oompaBase "oompaBase" "3.2.10"
openssl "openssl" "2.3.3"
org.Hs.eg.db "org.Hs.eg.db" "3.20.0"
org.Mm.eg.db "org.Mm.eg.db" "3.20.0"
paletteer "paletteer" "1.6.0"
palr "palr" "0.4.0"
pals "pals" "1.10"
parallel "parallel" "4.4.3"
parallelDist "parallelDist" "0.2.6"
parallelly "parallelly" "1.45.1"
parsnip "parsnip" "1.3.2"
patchwork "patchwork" "1.3.1"
pbdZMQ "pbdZMQ" "0.3-14"
pbkrtest "pbkrtest" "0.5.5"
pheatmap "pheatmap" "1.0.13"
pillar "pillar" "1.11.0"
pkgbuild "pkgbuild" "1.4.8"
pkgconfig "pkgconfig" "2.0.3"
pkgdown "pkgdown" "2.1.3"
pkgload "pkgload" "1.4.0"
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" "0.15.1"
promises "promises" "1.3.2"
ProtGenerics "ProtGenerics" "1.38.0"
proxy "proxy" "0.4-27"
ps "ps" "1.9.1"
purrr "purrr" "1.1.0"
quadprog "quadprog" "1.5-8"
quantmod "quantmod" "0.4.28"
quantreg "quantreg" "6.00"
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" "1.4.0"
randomForest "randomForest" "4.7-1.2"
rappdirs "rappdirs" "0.3.3"
rbibutils "rbibutils" "2.3"
rcmdcheck "rcmdcheck" "1.4.0"
RColorBrewer "RColorBrewer" "1.1-3"
Rcpp "Rcpp" "1.1.0"
RcppArmadillo "RcppArmadillo" "14.6.0-1"
RcppEigen "RcppEigen" "0.3.4.0.2"
RcppNumerical "RcppNumerical" "0.6-0"
RcppParallel "RcppParallel" "5.1.9"
RCurl "RCurl" "1.98-1.16"
Rdpack "Rdpack" "2.6.4"
reactome.db "reactome.db" "1.89.0"
ReactomePA "ReactomePA" "1.50.0"
readr "readr" "2.1.5"
readxl "readxl" "1.4.5"
recipes "recipes" "1.3.1"
reformulas "reformulas" "0.4.1"
remaCor "remaCor" "0.0.18"
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" "1.4.4"
restfulr "restfulr" "0.0.16"
rex "rex" "1.2.1"
rgl "rgl" "1.3.24"
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" "2.29"
RobustRankAggreg "RobustRankAggreg" "1.2.1"
RODBC "RODBC" "1.3-26"
roxygen2 "roxygen2" "7.3.2"
rpart "rpart" "4.1.24"
rprojroot "rprojroot" "2.1.0"
rsample "rsample" "1.3.1"
Rsamtools "Rsamtools" "2.22.0"
RSQLite "RSQLite" "2.4.2"
rstatix "rstatix" "0.7.2"
rstudioapi "rstudioapi" "0.17.1"
rsvd "rsvd" "1.0.5"
rtracklayer "rtracklayer" "1.66.0"
rversions "rversions" "2.1.2"
rvest "rvest" "1.0.4"
S4Arrays "S4Arrays" "1.6.0"
S4Vectors "S4Vectors" "0.44.0"
S7 "S7" "0.2.0"
sass "sass" "0.4.10"
ScaledMatrix "ScaledMatrix" "1.14.0"
scales "scales" "1.4.0"
scatterpie "scatterpie" "0.2.5"
scico "scico" "1.5.0"
scuttle "scuttle" "1.16.0"
selectr "selectr" "0.4-2"
sessioninfo "sessioninfo" "1.2.3"
sfd "sfd" "0.1.0"
shape "shape" "1.4.6.1"
shiny "shiny" "1.11.1"
SingleCellExperiment "SingleCellExperiment" "1.28.0"
slider "slider" "0.3.2"
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" "1.5.0"
stats "stats" "4.4.3"
stats4 "stats4" "4.4.3"
stringi "stringi" "1.8.7"
stringr "stringr" "1.5.1"
styler "styler" "1.10.3"
SummarizedExperiment "SummarizedExperiment" "1.36.0"
survival "survival" "3.8-3"
sys "sys" "3.4.3"
systemfonts "systemfonts" "1.2.3"
tcltk "tcltk" "4.4.3"
testthat "testthat" "3.2.3"
textshaping "textshaping" "1.0.1"
tibble "tibble" "3.3.0"
tidygraph "tidygraph" "1.3.0"
tidymodels "tidymodels" "1.3.0"
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" "4041.110"
tinytex "tinytex" "0.57"
tools "tools" "4.4.3"
treeio "treeio" "1.30.0"
truncnorm "truncnorm" "1.0-9"
tseries "tseries" "0.10-58"
TTR "TTR" "0.24.4"
tune "tune" "1.3.0"
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" "3.1.0"
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" "1.6.5"
vsn "vsn" "3.74.0"
waldo "waldo" "0.6.2"
warp "warp" "0.2.1"
whisker "whisker" "0.4.1"
withr "withr" "3.0.2"
workflows "workflows" "1.2.0"
workflowsets "workflowsets" "1.1.1"
writexl "writexl" "1.5.4"
xfun "xfun" "0.52"
XML "XML" "3.99-0.17"
xml2 "xml2" "1.3.8"
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" "2.3.10"
yardstick "yardstick" "1.3.2"
yulab.utils "yulab.utils" "0.2.0"
zip "zip" "2.3.3"
zlibbioc "zlibbioc" "1.52.0"
zoo "zoo" "1.8-14"
>
>
julia -E 'using InteractiveUtils; versioninfo()':
Julia Version 1.11.6
Commit 9615af0f269 (2025-07-09 12:58 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-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 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/v1.11/Project.toml`
[f67ccb44] HDF5 v0.17.2
[7073ff75] IJulia v1.29.2
[c3e4b0f8] Pluto v0.20.13
nothing