- Version: 4.4.0 and 4.3.0
- Additional R packages (to be listed):
- BiocManager == 1.30.27
- CCprofiler == 0.99.1
- clusterProfiler == 4.12.6
- cowplot == 1.2.0
- data.table == 1.17.8
- DESeq2 == 1.44.0
- devtools == 2.4.6
- dplyr == 1.1.4
- fgsea == 1.30.0
- ggplot2 == 4.0.0
- ggraphy == 2.2.2
- ggrepel == 0.9.6
- ggVennDiagram == 1.5.4
- GP.db == 3.19.1
- RColorBrewer == 1.1-3
- rstudioapi == 0.17.1
- jsonlite == 2.0.0
- MultiAssayExperiment == 1.30.3
- magrittr == 2.0.4
- farver == 2.1.2
- MALDIquant == 1.22.3
- rmarkdown == 2.30
- zlibbioc == 1.50.0
- vctrs == 0.6.5
- base64enc == 0.1-3
- htmltools == 0.5.8.1
- S4Arrays == 1.4.1
- progress == 1.2.3
- curl == 7.0.0
- SparseArray == 1.4.8
- Formula == 1.2-5
- mzID == 1.42.0
- TTR == 0.24.4
- pracma == 2.4.6
- htmlwidgets == 1.6.4
- naivebayes == 1.0.0
- plyr == 1.8.9
- impute == 1.78.0
- zoo == 1.8-14
- igraph == 2.2.1
- lifecycle == 1.0.4
- iterators == 1.0.14
- pkgconfig == 2.0.3
- Matrix == 1.7-0
- R6 == 2.6.1
- fastmap == 1.2.0
- GenomeInfoDbData == 1.2.12
- rbibutils == 2.4
- MatrixGenerics == 1.16.0
- clue == 0.3-66
- digest == 0.6.39
- pcaMethods == 1.96.0
- colorspace == 2.1-2
- S4Vectors == 0.42.1
- Hmisc == 5.2-4
- GenomicRanges == 1.56.2
- httr == 1.4.7
- abind == 1.4-8
- compiler == 4.4.0
- withr == 3.0.2
- doParallel == 1.0.17
- speedglm == 0.3-5
- htmlTable == 2.4.3
- S7 == 0.2.0
- backports == 1.5.0
- tseries == 0.10-58
- BiocParallel == 1.36.0
- DBI == 1.2.3
- biglm == 0.9-3
- R.utils == 2.13.0
- LiblineaR == 2.10-24
- MASS == 7.3-60.2
- DelayedArray == 0.30.1
- mzR == 2.38.0
- tools == 4.4.0
- PSMatch == 1.8.0
- foreign == 0.8-86
- lmtest == 0.9-40
- ranger == 0.17.0
- quantmod == 0.4.28
- nnet == 7.3-19
- R.oo == 1.27.1
- glue == 1.8.0
- quadprog == 1.5-8
- nlme == 3.1-164
- QFeatures == 1.14.2
- grid == 4.4.0
- checkmate == 2.3.3
- cluster == 2.1.6
- reshape2 == 1.4.4
- snow == 0.4-4
- generics == 0.1.4
- gtable == 0.3.6
- R.methodsS3 == 1.8.2
- preprocessCore == 1.66.0
- tidyr == 1.3.1
- hms == 1.1.4
- XVector == 0.44.0
- BiocGenerics == 0.54.1
- foreach == 1.5.2
- pillar == 1.11.1
- stringr == 1.6.0
- limma == 3.60.6
- splines == 4.4.0
- robustbase == 0.99-6
- lattice == 0.22-6
- gmp == 0.7-5
- tidyselect == 1.2.1
- knitr == 1.50
- gridExtra == 2.3
- urca == 1.3-4
- IRanges == 2.38.1
- ProtGenerics == 1.36.0
- SummarizedExperiment == 1.34.0
- forecast == 8.24.0
- stats4 == 4.4.0
- xfun == 0.54
- Biobase == 2.64.0
- statmod == 1.5.1
- MSnbase == 2.30.1
- timeDate == 4051.111
- matrixStats == 1.5.0
- DEoptimR == 1.1-4
- pheatmap == 1.0.13
- stringi == 1.8.7
- UCSC.utils == 1.0.0
- lazyeval == 0.2.2
- evaluate == 1.0.5
- codetools == 0.2-20
- tester == 0.3.0
- qvalue == 2.36.0
- MsCoreUtils == 1.16.1
- tibble == 3.3.0
- BiocManager == 1.30.27
- cli == 3.6.2
- affyio == 1.74.0
- rpart == 4.1.23
- Rdpack == 2.6.4
- Rcpp == 1.1.0
- GenomeInfoDb == 1.40.1
- doSNOW == 1.0.20
- XML == 3.99-0.20
- parallel == 4.4.0
- fracdiff == 1.5-3
- prettyunits == 1.2.0
- AnnotationFilter == 1.28.0
- Rmpfr == 1.1-2
- scales == 1.4.0
- xts == 0.14.1
- affy == 1.82.0
- ncdf4 == 1.24
- purrr == 1.1.0
- crayon == 1.5.3
- rlang == 1.1.3
- vsn == 3.72.0
- PrInCE == 1.20.0
- Version: 3.8.3 and 3.9.21
- Additional Python packages (to be listed):
- alabaster == 0.7.12
- anaconda-client == 1.11.0
- anaconda-navigator == 2.3.1
- anaconda-project == 0.11.1
- anyio == 3.5.0
- appdirs == 1.4.4
- argon2-cffi == 21.3.0
- argon2-cffi-bindings == 21.2.0
- arrow == 1.2.2
- astroid == 2.11.7
- astropy == 5.1
- atomicwrites == 1.4.0
- attrs == 21.4.0
- Automat == 20.2.0
- autopep8 == 1.6.0
- Babel == 2.9.1
- backcall == 0.2.0
- backports.functools-lru-cache == 1.6.4
- backports.tempfile == 1.0
- backports.weakref == 1.0.post1
- bcrypt == 3.2.0
- beautifulsoup4 == 4.11.1
- binaryornot == 0.4.4
- biopython == 1.79
- bitarray == 2.5.1
- bkcharts == 0.2
- black == 22.6.0
- bleach == 4.1.0
- bokeh == 2.4.3
- boto3 == 1.24.28
- botocore == 1.27.28
- Bottleneck == 1.3.5
- brotlipy == 0.7.0
- certifi == 2022.9.14
- cffi == 1.15.1
- chardet == 4.0.0
- charset-normalizer == 2.0.4
- click == 8.0.4
- cloudpickle == 2.0.0
- clyent == 1.2.2
- colorama == 0.4.5
- colorcet == 3.0.0
- comtypes == 1.1.10
- conda == 22.9.0
- conda-build == 3.22.0
- conda-content-trust == 0.1.3
- conda-pack == 0.6.0
- conda-package-handling == 1.9.0
- conda-repo-cli == 1.0.20
- conda-token == 0.4.0
- conda-verify == 3.4.2
- constantly == 15.1.0
- cookiecutter == 1.7.3
- cramjam == 2.10.0
- cryptography == 37.0.1
- cssselect == 1.1.0
- cycler == 0.11.0
- Cython == 0.29.32
- cytoolz == 0.11.0
- daal4py == 2021.6.0
- dask == 2022.7.0
- datashader == 0.14.1
- datashape == 0.5.4
- debugpy == 1.5.1
- decorator == 5.1.1
- defusedxml == 0.7.1
- diff-match-patch == 20200713
- dill == 0.3.4
- distributed == 2022.7.0
- docutils == 0.18.1
- easypqp == 0.1.42
- entrypoints == 0.4
- et-xmlfile == 1.1.0
- fastjsonschema == 2.16.2
- filelock == 3.6.0
- flake8 == 4.0.1
- Flask == 1.1.2
- fonttools == 4.25.0
- fsspec == 2022.7.1
- future == 0.18.2
- gensim == 4.1.2
- glob2 == 0.7
- greenlet == 1.1.1
- h5py == 3.7.0
- HeapDict == 1.0.1
- holoviews == 1.15.0
- hvplot == 0.8.0
- hyperlink == 21.0.0
- idna == 3.3
- imagecodecs == 2021.8.26
- imageio == 2.19.3
- imagesize == 1.4.1
- importlib-metadata == 4.11.3
- incremental == 21.3.0
- inflection == 0.5.1
- iniconfig == 1.1.1
- install == 1.3.5
- intake == 0.6.5
- intervaltree == 3.1.0
- ipykernel == 6.15.2
- ipython == 7.31.1
- ipython-genutils == 0.2.0
- ipywidgets == 7.6.5
- isort == 5.9.3
- itemadapter == 0.3.0
- itemloaders == 1.0.4
- itsdangerous == 2.0.1
- jdcal == 1.4.1
- jedi == 0.18.1
- jellyfish == 0.9.0
- Jinja2 == 2.11.3
- jinja2-time == 0.2.0
- jmespath == 0.10.0
- joblib == 1.1.0
- json5 == 0.9.6
- jsonschema == 4.16.0
- jupyter == 1.0.0
- jupyter_client == 7.3.4
- jupyter-console == 6.4.3
- jupyter_core == 4.11.1
- jupyter-server == 1.18.1
- jupyterlab == 3.4.4
- jupyterlab-pygments == 0.1.2
- jupyterlab-server == 2.10.3
- jupyterlab-widgets == 1.0.0
- keyring == 23.4.0
- kiwisolver == 1.4.2
- lazy-object-proxy == 1.6.0
- libarchive-c == 2.9
- llvmlite == 0.38.0
- locket == 1.0.0
- lxml == 4.9.1
- lz4 == 3.1.3
- Markdown == 3.3.4
- MarkupSafe == 2.0.1
- matplotlib == 3.5.2
- matplotlib-inline == 0.1.6
- mccabe == 0.6.1
- menuinst == 1.4.19
- mistune == 0.8.4
- mkl-fft == 1.3.1
- mkl-random == 1.2.2
- mkl-service == 2.4.0
- mock == 4.0.3
- mpmath == 1.2.1
- msgpack == 1.0.3
- multipledispatch == 0.6.0
- munkres == 1.1.4
- mypy-extensions == 0.4.3
- navigator-updater == 0.3.0
- nbclassic == 0.3.5
- nbclient == 0.5.13
- nbconvert == 6.4.4
- nbformat == 5.5.0
- nest-asyncio == 1.5.5
- networkx == 2.8.4
- nltk == 3.7
- nose == 1.3.7
- notebook == 6.4.12
- numba == 0.55.1
- numexpr == 2.8.3
- numpy == 2.0.2
- numpydoc == 1.4.0
- olefile == 0.46
- openpyxl == 3.0.10
- packaging == 21.3
- pandas == 2.2.3
- pandocfilters == 1.5.0
- panel == 0.13.1
- param == 1.12.0
- paramiko == 2.8.1
- parsel == 1.6.0
- parso == 0.8.3
- partd == 1.2.0
- pathlib == 1.0.1
- pathspec == 0.9.0
- patsy == 0.5.2
- pep8 == 1.7.1
- pexpect == 4.8.0
- pickleshare == 0.7.5
- Pillow == 9.2.0
- pip == 22.2.2
- pkginfo == 1.8.2
- platformdirs == 2.5.2
- plotly == 5.9.0
- pluggy == 1.0.0
- poyo == 0.5.0
- prometheus-client == 0.14.1
- prompt-toolkit == 3.0.20
- Protego == 0.1.16
- psutil == 5.9.0
- ptyprocess == 0.7.0
- py == 1.11.0
- pyarrow == 20.0.0
- pyasn1 == 0.4.8
- pyasnn-modules == 0.2.8
- pycodestyle == 2.8.0
- pycosat == 0.6.3
- pycparser == 2.21
- pyct == 0.4.8
- pycurl == 7.45.1
- PyDispatcher == 2.0.5
- pydocstyle == 6.1.1
- pyerfa == 2.0.0
- pyflakes == 2.4.0
- Pygments == 2.11.2
- PyHamcrest == 2.0.2
- PyJWT == 2.4.0
- pylint == 2.14.5
- pyls-spyder == 0.4.0
- PyNaCl == 1.5.0
- pyodbc == 4.0.34
- pyopenms == 3.1.0
- pyOpenSSL == 22.0.0
- pyparsing == 3.0.9
- pyrsistent == 0.18.0
- PySocks == 1.7.1
- pytest == 7.1.2
- python-dateutil == 2.8.2
- python-lsp-black == 1.0.0
- python-lsp-jsonrpc == 1.0.0
- python-lsp-server == 1.3.3
- python-slugify == 5.0.2
- python-snappy == 0.6.0
- pytz == 2022.1
- pyviz-comms == 2.0.2
- PyWavelets == 1.3.0
- pywin32 == 302
- pywin32-ctypes == 0.2.0
- pywinpty == 2.0.2
- PyYAML == 6.0
- pyzmq == 23.2.0
- QDarkStyle == 3.0.2
- qstylizer == 0.1.10
- QtAwesome == 1.0.3
- qtconsole == 5.2.2
- QtPy == 2.2.0
- queuelib == 1.5.0
- regex == 2022.7.9
- requests == 2.28.1
- requests-file == 1.5.1
- rope == 0.22.0
- Rtree == 0.9.7
- ruamel-yaml-conda == 0.15.100
- s3transfer == 0.6.0
- scikit-image == 0.19.2
- scikit-learn == 1.0.2
- scikit-learn-intelex == 2021.20221004.171935
- scipy == 1.9.1
- Scrapy == 2.6.2
- seaborn == 0.11.2
- Send2Trash == 1.8.0
- service-identity == 18.1.0
- setuptools == 63.4.1
- sip == 4.19.13
- six == 1.16.0
- smart-open == 5.2.1
- sniffio == 1.2.0
- snowballstemmer == 2.2.0
- sortedcollections == 2.1.0
- sortedcontainers == 2.4.0
- soupsieve == 2.3.1
- Sphinx == 5.0.2
- sphinxcontrib-applehelp == 1.0.2
- sphinxcontrib-devhelp == 1.0.2
- sphinxcontrib-htmlhelp == 2.0.0
- sphinxcontrib-jsmath == 1.0.1
- sphinxcontrib-qthelp == 1.0.3
- sphinxcontrib-serializinghtml == 1.1.5
- spyder == 5.2.2
- spyder-kernels == 2.2.1
- SQLAlchemy == 1.4.39
- statsmodels == 0.13.2
- sympy == 1.10.1
- tables == 3.6.1
- tabulate == 0.8.10
- TBB == 0.2
- tblib == 1.7.0
- tenacity == 8.0.1
- terminado == 0.13.1
- testpath == 0.6.0
- text-unidecode == 1.3
- textdistance == 4.2.1
- threadpoolctl == 2.2.0
- three-merge == 0.1.1
- tifffile == 2021.7.2
- tinycss == 0.4
- tldextract == 3.2.0
- toml == 0.10.2
- tomli == 2.0.1
- tomlkit == 0.11.1
- toolz == 0.11.2
- tornado == 6.1
- tqdm == 4.64.1
- traitlets == 5.1.1
- Twisted == 22.2.0
- twisted-iocpsupport == 1.0.2
- typing_extensions == 4.3.0
- tzdata == 2025.2
- ujson == 5.4.0
- Unidecode == 1.2.0
- urllib3 == 1.26.11
- w3lib == 1.21.0
- watchdog == 2.1.6
- wcwidth == 0.2.5
- webencodings == 0.5.1
- websocket-client == 0.58.0
- Werkzeug == 2.0.3
- wheel == 0.37.1
- widgetsnbextension == 3.5.2
- win-inet-pton == 1.1.0
- win-unicode-console == 0.5
- wincertstore == 0.2
- wrapt == 1.14.1
- xarray == 0.20.1
- xlrd == 2.0.1
- XlsxWriter == 3.0.3
- xlwings == 0.27.15
- yapf == 0.31.0
- zict == 2.1.0
- zipp == 3.8.0
- zope.interface == 5.4.0