Pre-installed tools on Researcher Workbench

  • Updated

Below you can find a list of tools that come pre-installed when opening a Jupyter Notebook within the Researcher Workbench’s Cloud Analysis Environment. We recommend utilizing the “Ctrl/Command + F” function for quick searching.

You can also produce these lists your self within a notebook by running the below commands:

Python modules (conda list)

# packages in environment at /opt/conda:

 

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
absl-py                   1.4.0                    pypi_0    pypi
aiodns                    2.0.0                    pypi_0    pypi
aiohttp                   3.8.5           py310h2372a71_0    conda-forge
aiohttp-cors              0.7.0                    pypi_0    pypi
aiorwlock                 1.3.0                    pypi_0    pypi
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
ansiwrap                  0.8.4                    pypi_0    pypi
anyio                     3.7.1              pyhd8ed1ab_0    conda-forge
apache-beam               2.46.0                   pypi_0    pypi
argcomplete               3.1.2                    pypi_0    pypi
argon2-cffi               23.1.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
array-record              0.4.1                    pypi_0    pypi
arrow                     1.2.3              pyhd8ed1ab_0    conda-forge
arviz                     0.12.1                   pypi_0    pypi
astroid                   3.0.0                    pypi_0    pypi
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3                    pypi_0    pypi
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
asyncinit                 0.2.4                    pypi_0    pypi
attrs                     23.1.0             pyh71513ae_1    conda-forge
avro                      1.11.3                   pypi_0    pypi
azure-common              1.1.28                   pypi_0    pypi
azure-core                1.29.4                   pypi_0    pypi
azure-identity            1.14.0                   pypi_0    pypi
azure-mgmt-core           1.4.0                    pypi_0    pypi
azure-mgmt-storage        20.1.0                   pypi_0    pypi
azure-storage-blob        12.18.3                  pypi_0    pypi
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backoff                   2.2.1                    pypi_0    pypi
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beatrix-jupyterlab        2023.814.150030          pypi_0    pypi
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bgzip                     0.3.5                    pypi_0    pypi
biopython                 1.81                     pypi_0    pypi
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blessed                   1.20.0                   pypi_0    pypi
bokeh                     3.2.2                    pypi_0    pypi
boltons                   23.0.0             pyhd8ed1ab_0    conda-forge
boto3                     1.28.75                  pypi_0    pypi
botocore                  1.31.75                  pypi_0    pypi
brewer2mpl                1.4.1                    pypi_0    pypi
brotlipy                  0.7.0           py310h7f8727e_1002  
bx-python                 0.10.0                   pypi_0    pypi
bzip2                     1.0.8                h7b6447c_0  
c-ares                    1.19.1               hd590300_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cachecontrol              0.13.1                   pypi_0    pypi
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                4.2.4                    pypi_0    pypi
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
cftime                    1.6.2                    pypi_0    pypi
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
cli-builder               0.1.5                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloud-tpu-client          0.10                     pypi_0    pypi
cloud-tpu-profiler        2.4.0                    pypi_0    pypi
cloudpickle               2.2.1                    pypi_0    pypi
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
coloredlogs               15.0.1                   pypi_0    pypi
colorful                  0.5.5                    pypi_0    pypi
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
commonmark                0.9.1                    pypi_0    pypi
conda                     23.7.3          py310hff52083_0    conda-forge
conda-content-trust       0+unknown                pypi_0    pypi
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
contourpy                 1.1.0                    pypi_0    pypi
crcmod                    1.7                      pypi_0    pypi
cromshell                 2.0.0                    pypi_0    pypi
cryptography              41.0.3          py310h75e40e8_0    conda-forge
cwl-upgrader              1.2.9                    pypi_0    pypi
cwl-utils                 0.29                     pypi_0    pypi
cwltool                   3.1.20230906142556          pypi_0    pypi
cycler                    0.12.0                   pypi_0    pypi
cython                    0.29.36                  pypi_0    pypi
daal                      2023.2.1                 pypi_0    pypi
daal4py                   2023.2.1                 pypi_0    pypi
dacite                    1.8.1                    pypi_0    pypi
db-dtypes                 1.1.1                    pypi_0    pypi
debugpy                   1.6.7.post1              pypi_0    pypi
decorator                 4.4.2                    pypi_0    pypi
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecat                  2.1.1                    pypi_0    pypi
deprecated                1.2.14                   pypi_0    pypi
dill                      0.3.7                    pypi_0    pypi
distlib                   0.3.7                    pypi_0    pypi
dlenv-tf-2-11-gpu         1.0.20230823    py310hfd508a8_0    file:///tmp/conda
dm-tree                   0.1.8                    pypi_0    pypi
docker                    6.1.3                    pypi_0    pypi
docopt                    0.6.2                    pypi_0    pypi
docstring-parser          0.15                     pypi_0    pypi
dsub                      0.3.6                    pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
etils                     1.4.1                    pypi_0    pypi
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
explainable-ai-sdk        1.3.3                    pypi_0    pypi
fastapi                   0.101.1                  pypi_0    pypi
fastavro                  1.8.2                    pypi_0    pypi
fasteners                 0.18                     pypi_0    pypi
fastinterval              0.1.1                    pypi_0    pypi
fastprogress              1.0.3                    pypi_0    pypi
filelock                  3.12.2                   pypi_0    pypi
firecloud                 0.16.35                  pypi_0    pypi
flatbuffers               23.5.26                  pypi_0    pypi
flit-core                 3.9.0              pyhd8ed1ab_0    conda-forge
fonttools                 4.42.1                   pypi_0    pypi
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
frozenlist                1.4.0           py310h2372a71_0    conda-forge
fsspec                    2023.6.0                 pypi_0    pypi
gast                      0.4.0                    pypi_0    pypi
gatkpythonpackages        0.1                      pypi_0    pypi
gcsfs                     2023.6.0                 pypi_0    pypi
getm                      0.0.5                    pypi_0    pypi
ggplot                    0.11.5                   pypi_0    pypi
gitdb                     4.0.10                   pypi_0    pypi
gitpython                 3.1.32                   pypi_0    pypi
gnomad                    0.6.4                    pypi_0    pypi
google-api-core           1.34.0                   pypi_0    pypi
google-api-core-grpc      2.11.1               hd8ed1ab_0    conda-forge
google-api-python-client  1.8.0                    pypi_0    pypi
google-apitools           0.5.31                   pypi_0    pypi
google-auth               2.22.0             pyh1a96a4e_0    conda-forge
google-auth-httplib2      0.1.0                    pypi_0    pypi
google-auth-oauthlib      0.8.0                    pypi_0    pypi
google-cloud-aiplatform   1.31.0                   pypi_0    pypi
google-cloud-artifact-registry 1.8.3                    pypi_0    pypi
google-cloud-bigquery     2.34.4                   pypi_0    pypi
google-cloud-bigquery-datatransfer 3.12.1                   pypi_0    pypi
google-cloud-bigquery-storage 2.16.2                   pypi_0    pypi
google-cloud-bigtable     1.7.3                    pypi_0    pypi
google-cloud-core         2.3.3              pyhd8ed1ab_0    conda-forge
google-cloud-datastore    1.15.5             pyhd8ed1ab_0    conda-forge
google-cloud-dlp          3.12.2                   pypi_0    pypi
google-cloud-language     1.3.2                    pypi_0    pypi
google-cloud-monitoring   2.15.1                   pypi_0    pypi
google-cloud-pubsub       2.18.3                   pypi_0    pypi
google-cloud-pubsublite   1.8.3                    pypi_0    pypi
google-cloud-recommendations-ai 0.7.1                    pypi_0    pypi
google-cloud-resource-manager 1.10.4                   pypi_0    pypi
google-cloud-spanner      3.40.1                   pypi_0    pypi
google-cloud-storage      1.44.0                   pypi_0    pypi
google-cloud-videointelligence 1.16.3                   pypi_0    pypi
google-cloud-vision       3.4.4                    pypi_0    pypi
google-crc32c             1.5.0                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
google-resumable-media    2.6.0                    pypi_0    pypi
googleapis-common-protos  1.60.0             pyhd8ed1ab_0    conda-forge
gpustat                   1.0.0                    pypi_0    pypi
greenlet                  2.0.2                    pypi_0    pypi
grpc-cpp                  1.48.1               hc2bec63_1    conda-forge
grpc-google-iam-v1        0.12.6                   pypi_0    pypi
grpcio                    1.57.0                   pypi_0    pypi
grpcio-status             1.48.2                   pypi_0    pypi
gs-chunked-io             0.5.2                    pypi_0    pypi
gviz-api                  1.10.0                   pypi_0    pypi
gymnasium                 0.26.3                   pypi_0    pypi
gymnasium-notices         0.0.1                    pypi_0    pypi
h11                       0.14.0                   pypi_0    pypi
h5py                      3.9.0                    pypi_0    pypi
hail                      0.2.126                  pypi_0    pypi
hdbscan                   0.8.33                   pypi_0    pypi
hdfs                      2.7.2                    pypi_0    pypi
html5lib                  1.1                      pypi_0    pypi
htmlmin                   0.1.12                   pypi_0    pypi
httplib2                  0.21.0                   pypi_0    pypi
humanfriendly             10.0                     pypi_0    pypi
humanize                  1.1.0                    pypi_0    pypi
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
igv-jupyter               1.0.0                    pypi_0    pypi
imagehash                 4.3.1                    pypi_0    pypi
imageio                   2.31.1                   pypi_0    pypi
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.0.1              pyhd8ed1ab_0    conda-forge
intel-openmp              2023.2.0                 pypi_0    pypi
ipykernel                 6.25.1             pyh71e2992_0    conda-forge
ipython                   8.14.0             pyh41d4057_0    conda-forge
ipython-genutils          0.2.0                    pypi_0    pypi
ipython-sql               0.5.0                    pypi_0    pypi
ipywidgets                8.1.0                    pypi_0    pypi
isal                      1.5.1                    pypi_0    pypi
isodate                   0.6.1                    pypi_0    pypi
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
isort                     5.12.0                   pypi_0    pypi
janus                     1.0.0                    pypi_0    pypi
jaraco-classes            3.3.0                    pypi_0    pypi
jedi                      0.19.0             pyhd8ed1ab_0    conda-forge
jeepney                   0.8.0                    pypi_0    pypi
jinja2                    3.0.3                    pypi_0    pypi
jmespath                  0.10.0                   pypi_0    pypi
joblib                    1.3.2                    pypi_0    pypi
jproperties               2.1.1                    pypi_0    pypi
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpatch                 1.32               pyhd8ed1ab_0    conda-forge
jsonpointer               2.0                        py_0    conda-forge
jsonschema                4.19.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.19.0             pyhd8ed1ab_1    conda-forge
jupyter-client            7.4.9                    pypi_0    pypi
jupyter-contrib-core      0.4.2                    pypi_0    pypi
jupyter-contrib-nbextensions 0.7.0                    pypi_0    pypi
jupyter-highlight-selected-word 0.2.0                    pypi_0    pypi
jupyter-http-over-ws      0.0.8                    pypi_0    pypi
jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge
jupyter-nbextensions-configurator 0.6.3                    pypi_0    pypi
jupyter-server            1.24.0                   pypi_0    pypi
jupyter-server-mathjax    0.2.6                    pypi_0    pypi
jupyter-server-proxy      4.0.0                    pypi_0    pypi
jupyter_client            8.3.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.1           py310hff52083_0    conda-forge
jupyter_events            0.7.0              pyhd8ed1ab_2    conda-forge
jupyter_server            2.7.1              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                3.4.8                    pypi_0    pypi
jupyterlab-git            0.42.0                   pypi_0    pypi
jupyterlab-server         2.23.0                   pypi_0    pypi
jupyterlab-widgets        3.0.8                    pypi_0    pypi
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.24.0             pyhd8ed1ab_0    conda-forge
jupytext                  1.15.0                   pypi_0    pypi
keras                     2.11.0                   pypi_0    pypi
keras-tuner               1.3.5                    pypi_0    pypi
keyring                   24.2.0                   pypi_0    pypi
keyrings-google-artifactregistry-auth 1.1.2                    pypi_0    pypi
kfp                       2.0.1                    pypi_0    pypi
kfp-pipeline-spec         0.2.2                    pypi_0    pypi
kfp-server-api            2.0.1                    pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
kt-legacy                 1.0.5                    pypi_0    pypi
kubernetes                26.1.0                   pypi_0    pypi
lazy-loader               0.3                      pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libabseil                 20220623.0      cxx17_h05df665_6    conda-forge
libclang                  16.0.6                   pypi_0    pypi
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libprotobuf               3.20.3               h3eb15da_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.44.2               hd590300_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvmlite                  0.40.1                   pypi_0    pypi
lxml                      4.9.3                    pypi_0    pypi
lz4                       4.3.2                    pypi_0    pypi
mako                      1.2.4                    pypi_0    pypi
markdown                  3.4.4                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.3           py310h2372a71_0    conda-forge
matplotlib                3.7.2                    pypi_0    pypi
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
matplotlib-venn           0.11.9                   pypi_0    pypi
mccabe                    0.7.0                    pypi_0    pypi
mdit-py-plugins           0.4.0                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
mistune                   2.0.5                    pypi_0    pypi
mizani                    0.9.2                    pypi_0    pypi
mkl                       2023.2.0                 pypi_0    pypi
mock                      5.1.0                    pypi_0    pypi
more-itertools            10.1.0                   pypi_0    pypi
msal                      1.24.1                   pypi_0    pypi
msal-extensions           1.0.0                    pypi_0    pypi
msgpack                   1.0.5                    pypi_0    pypi
msrest                    0.7.1                    pypi_0    pypi
multidict                 6.0.4           py310h1fa729e_0    conda-forge
multimethod               1.9.1                    pypi_0    pypi
multiprocess              0.70.15                  pypi_0    pypi
mypy-extensions           1.0.0                    pypi_0    pypi
nb_conda                  2.2.1                    unix_6    conda-forge
nb_conda_kernels          2.3.1           py310hff52083_2    conda-forge
nbclassic                 0.4.8                    pypi_0    pypi
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.7.4              pyhd8ed1ab_0    conda-forge
nbdime                    3.2.0                    pypi_0    pypi
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
nbstripout                0.6.1                    pypi_0    pypi
ncurses                   6.4                  hcb278e6_0    conda-forge
nest-asyncio              1.5.7                    pypi_0    pypi
netcdf4                   1.6.4                    pypi_0    pypi
networkx                  3.1                      pypi_0    pypi
nodejs                    20.5.1               hf52ce11_0    conda-forge
nose                      1.3.7                    pypi_0    pypi
notebook                  6.5.4                    pypi_0    pypi
notebook-executor         0.2                      pypi_0    pypi
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numba                     0.57.1                   pypi_0    pypi
numpy                     1.22.1                   pypi_0    pypi
nvidia-ml-py              11.495.46                pypi_0    pypi
oauth2client              4.1.3                    pypi_0    pypi
oauthlib                  3.2.2                    pypi_0    pypi
objsize                   0.6.1                    pypi_0    pypi
opencensus                0.11.2                   pypi_0    pypi
opencensus-context        0.1.3                    pypi_0    pypi
openssl                   3.1.2                hd590300_0    conda-forge
opentelemetry-api         1.19.0                   pypi_0    pypi
opentelemetry-exporter-otlp 1.19.0                   pypi_0    pypi
opentelemetry-exporter-otlp-proto-common 1.19.0                   pypi_0    pypi
opentelemetry-exporter-otlp-proto-grpc 1.19.0                   pypi_0    pypi
opentelemetry-exporter-otlp-proto-http 1.19.0                   pypi_0    pypi
opentelemetry-proto       1.19.0                   pypi_0    pypi
opentelemetry-sdk         1.19.0                   pypi_0    pypi
opentelemetry-semantic-conventions 0.40b0                   pypi_0    pypi
opt-einsum                3.3.0                    pypi_0    pypi
orjson                    3.9.5                    pypi_0    pypi
overrides                 6.5.0                    pypi_0    pypi
packaging                 21.3                     pypi_0    pypi
pandas                    2.0.3                    pypi_0    pypi
pandas-gbq                0.17.9                   pypi_0    pypi
pandas-profiling          3.6.6                    pypi_0    pypi
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
papermill                 2.4.0                    pypi_0    pypi
parameterized             0.9.0                    pypi_0    pypi
parsimonious              0.10.0                   pypi_0    pypi
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3                    pypi_0    pypi
pdoc3                     0.10.0                   pypi_0    pypi
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
phik                      0.12.3                   pypi_0    pypi
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.0                   pypi_0    pypi
pip                       23.3.1                   pypi_0    pypi
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.10.0             pyhd8ed1ab_0    conda-forge
plotly                    5.16.1                   pypi_0    pypi
plotnine                  0.10.1                   pypi_0    pypi
pluggy                    1.2.0              pyhd8ed1ab_0    conda-forge
portalocker               2.8.2                    pypi_0    pypi
prettytable               3.8.0                    pypi_0    pypi
prometheus_client         0.17.1             pyhd8ed1ab_0    conda-forge
promise                   2.3                      pypi_0    pypi
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
proto-plus                1.22.3                   pypi_0    pypi
protobuf                  3.20.2                   pypi_0    pypi
prov                      1.5.1                    pypi_0    pypi
psutil                    5.9.3                    pypi_0    pypi
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulp                      2.7.0                    pypi_0    pypi
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py-spy                    0.3.14                   pypi_0    pypi
py4j                      0.10.9.7                 pypi_0    pypi
pyarrow                   9.0.0                    pypi_0    pypi
pyasn1                    0.5.0                    pypi_0    pypi
pyasn1-modules            0.3.0                    pypi_0    pypi
pycares                   4.4.0                    pypi_0    pypi
pycosat                   0.6.4           py310h5764c6d_1    conda-forge
pycparser                 2.21                     pypi_0    pypi
pydantic                  1.10.12                  pypi_0    pypi
pydata-google-auth        1.8.2                    pypi_0    pypi
pydot                     1.4.2                    pypi_0    pypi
pyfaidx                   0.7.2.2                  pypi_0    pypi
pyfasta                   0.5.2                    pypi_0    pypi
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pyjwt                     2.8.0                    pypi_0    pypi
pylint                    3.0.0                    pypi_0    pypi
pymc3                     3.11.5                   pypi_0    pypi
pymongo                   3.13.0                   pypi_0    pypi
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pypandoc                  1.12                     pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
pysam                     0.22.0                   pypi_0    pypi
pysocks                   1.7.1           py310h06a4308_0  
python                    3.10.12         hd12c33a_0_cpython    conda-forge
python-datauri            2.1.0                    pypi_0    pypi
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.18.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-lzo                1.15                     pypi_0    pypi
python_abi                3.10                    3_cp310    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pyvcf3                    1.0.3                    pypi_0    pypi
pywavelets                1.4.1                    pypi_0    pypi
pyyaml                    6.0.1           py310h2372a71_0    conda-forge
pyzmq                     24.0.1                   pypi_0    pypi
ray                       2.6.3                    pypi_0    pypi
ray-cpp                   2.6.3                    pypi_0    pypi
rdflib                    7.0.0                    pypi_0    pypi
re2                       2022.06.01           h27087fc_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.30.2             pyhd8ed1ab_0    conda-forge
regex                     2023.8.8                 pypi_0    pypi
requests                  2.29.0                   pypi_0    pypi
requests-oauthlib         1.3.1                    pypi_0    pypi
requests-toolbelt         0.10.1                   pypi_0    pypi
retrying                  1.3.4                    pypi_0    pypi
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      12.6.0                   pypi_0    pypi
rpds-py                   0.9.2           py310hcb5633a_0    conda-forge
rsa                       4.9                pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.32         py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.7           py310h1fa729e_1    conda-forge
ruamel_yaml               0.15.100        py310h7f8727e_0  
s3transfer                0.7.0                    pypi_0    pypi
schema-salad              8.4.20230927144413          pypi_0    pypi
scikit-image              0.21.0                   pypi_0    pypi
scikit-learn              1.3.0                    pypi_0    pypi
scikit-learn-intelex      2023.2.1                 pypi_0    pypi
scipy                     1.7.3                    pypi_0    pypi
seaborn                   0.12.2                   pypi_0    pypi
secretstorage             3.3.3                    pypi_0    pypi
semver                    3.0.1                    pypi_0    pypi
send2trash                1.8.2              pyh41d4057_0    conda-forge
setuptools                68.1.2             pyhd8ed1ab_0    conda-forge
shapely                   1.8.5.post1              pypi_0    pypi
shellescape               3.8.1                    pypi_0    pypi
simpervisor               1.0.0                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
slackclient               2.5.0                    pypi_0    pypi
smart-open                6.3.0                    pypi_0    pypi
smmap                     5.0.0                    pypi_0    pypi
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0                    pypi_0    pypi
soupsieve                 2.4.1                    pypi_0    pypi
sqlalchemy                2.0.20                   pypi_0    pypi
sqlite                    3.38.2               hc218d9a_0  
sqlparse                  0.4.4                    pypi_0    pypi
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
starlette                 0.27.0                   pypi_0    pypi
statsmodels               0.14.0                   pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
tangled-up-in-unicode     0.2.0                    pypi_0    pypi
tbb                       2021.10.0                pypi_0    pypi
tenacity                  8.2.3                    pypi_0    pypi
tensorboard               2.11.2                   pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-profile 2.13.1                   pypi_0    pypi
tensorboard-plugin-wit    1.8.1                    pypi_0    pypi
tensorboardx              2.6.2                    pypi_0    pypi
tensorflow                2.11.0                   pypi_0    pypi
tensorflow-cloud          0.1.16                   pypi_0    pypi
tensorflow-datasets       4.9.0                    pypi_0    pypi
tensorflow-estimator      2.11.0                   pypi_0    pypi
tensorflow-hub            0.14.0                   pypi_0    pypi
tensorflow-io             0.29.0                   pypi_0    pypi
tensorflow-io-gcs-filesystem 0.29.0                   pypi_0    pypi
tensorflow-metadata       0.14.0                   pypi_0    pypi
tensorflow-probability    0.21.0                   pypi_0    pypi
tensorflow-serving-api    2.11.0                   pypi_0    pypi
tensorflow-transform      0.14.0                   pypi_0    pypi
termcolor                 2.3.0                    pypi_0    pypi
terminado                 0.17.1             pyh41d4057_0    conda-forge
terra-notebook-utils      0.13.0                   pypi_0    pypi
terra-widgets             0.0.1                    pypi_0    pypi
textwrap3                 0.9.2                    pypi_0    pypi
theano                    1.0.5                    pypi_0    pypi
theano-pymc               1.1.2                    pypi_0    pypi
threadpoolctl             3.2.0                    pypi_0    pypi
tifffile                  2023.8.12                pypi_0    pypi
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2                   pypi_0    pypi
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tomlkit                   0.12.1                   pypi_0    pypi
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.3.3           py310h2372a71_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typeguard                 2.13.3                   pypi_0    pypi
typer                     0.9.0                    pypi_0    pypi
typing-extensions         4.8.0                    pypi_0    pypi
typing_extensions         4.7.1              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023.3                   pypi_0    pypi
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
uritemplate               3.0.1                    pypi_0    pypi
urllib3                   1.26.16                  pypi_0    pypi
uvicorn                   0.23.2                   pypi_0    pypi
uvloop                    0.19.0                   pypi_0    pypi
virtualenv                20.21.0                  pypi_0    pypi
visions                   0.7.5                    pypi_0    pypi
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.6.2              pyhd8ed1ab_0    conda-forge
werkzeug                  3.0.0                    pypi_0    pypi
whatshap                  2.1                      pypi_0    pypi
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.8                    pypi_0    pypi
witwidget                 1.8.1                    pypi_0    pypi
wordcloud                 1.9.2                    pypi_0    pypi
wrapt                     1.15.0                   pypi_0    pypi
xarray                    2023.9.0                 pypi_0    pypi
xarray-einstats           0.6.0                    pypi_0    pypi
xgboost                   2.0.0                    pypi_0    pypi
xopen                     1.8.0                    pypi_0    pypi
xyzservices               2023.10.0                pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7b6447c_0  
yarl                      1.9.2           py310h2372a71_0    conda-forge
ydata-profiling           4.5.1                    pypi_0    pypi
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.16.2             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstandard                 0.19.0          py310h1275a96_2    conda-forge
zstd                      1.5.2                hfc55251_7    conda-forge

Note: you may need to restart the kernel to use updated packages.

 

R packages (installed.packages ())

abind 1.4-5
AnnotationDbi 1.62.2
AnnotationFilter 1.24.0
AnnotationHub 3.8.0
AnVIL 1.12.4
askpass 1.2.0
assertthat 0.2.1
backports 1.4.1
base 4.3.1
base64enc 0.1-3
beachmat 2.16.0
BH 1.81.0-1
bigrquery 1.4.2
Biobase 2.60.0
BiocFileCache 2.8.0
BiocGenerics 0.46.0
BiocIO 1.10.0
BiocManager 1.30.22
BiocNeighbors 1.18.0
BiocParallel 1.34.2
BiocSingular 1.16.0
BiocVersion 3.17.1
biomaRt 2.56.1
Biostrings 2.68.1
bit 4.0.5
bit64 4.0.5
bitops 1.0-7
blob 1.2.4
bluster 1.10.0
boot 1.3-28.1
brew 1.0-8
brio 1.1.3
broom 1.0.5
bslib 0.5.1
cachem 1.0.8
callr 3.7.3
caTools 1.18.2
cellranger 1.1.0
class 7.3-22
cli 3.6.1
clipr 0.8.0
cluster 2.1.4
codetools 0.2-19
colorspace 2.1-0
commonmark 1.9.0
compiler 4.3.1
conflicted 1.2.0
cowplot 1.1.1
cpp11 0.4.6
crayon 1.5.2
credentials 2.0.1
crosstalk 1.2.0
curl 5.1.0
data.table 1.14.8
datasets 4.3.1
DBI 1.1.3
dbplyr 2.3.4
DelayedArray 0.26.7
DelayedMatrixStats 1.22.6
deldir 1.0-9
desc 1.4.2
DESeq2 1.40.2
devtools 2.4.5
diffobj 0.3.5
digest 0.6.33
DNAcopy 1.74.1
downlit 0.4.3
dplyr 1.1.3
dqrng 0.3.1
DT 0.29
dtplyr 1.3.1
edgeR 3.42.4
ellipsis 0.3.2
ensembldb 2.24.1
evaluate 0.22
ExperimentHub 2.8.1
fansi 1.0.4
farver 2.1.1
fastmap 1.1.1
filelock 1.0.2
fitdistrplus 1.1-11
FNN 1.1.3.2
fontawesome 0.5.2
forcats 1.0.0
foreach 1.5.2
foreign 0.8-85
formatR 1.14
formula.tools 1.7.1
fs 1.6.3
futile.logger 1.4.3
futile.options 1.0.1
future 1.33.0
future.apply 1.11.0
gargle 1.5.2
gdsfmt 1.36.1
generics 0.1.3
GenomeInfoDb 1.36.4
GenomeInfoDbData 1.2.10
GenomicAlignments 1.36.0
GenomicFeatures 1.52.2
GenomicRanges 1.52.0
gert 2.0.0
ggplot2 3.4.3
ggrepel 0.9.3
ggridges 0.5.4
ggthemes 5.0.0
gh 1.4.0
gitcreds 0.1.2
glmnet 4.1-8
globals 0.16.2
glue 1.6.2
goftest 1.2-3
googleAuthR 2.0.1
googleCloudStorageR 0.7.0
googledrive 2.1.1
googlesheets4 1.1.1
gplots 3.1.3
graphics 4.3.1
grDevices 4.3.1
grid 4.3.1
gridExtra 2.3
gtable 0.3.4
gtools 3.9.4
GWASExactHW 1.01
haven 2.5.3
here 1.0.1
highr 0.10
hms 1.1.3
htmltools 0.5.6
htmlwidgets 1.6.2
httpuv 1.6.11
httr 1.4.7
httr2 0.2.3
hwriter 1.3.2.1
ica 1.0-3
ids 1.0.1
igraph 1.5.1
ini 0.3.1
interactiveDisplayBase 1.38.0
interp 1.1-4
Iranges 2.34.1
Irdisplay 1.1
Irkernel 1.3.2
irlba 2.3.5.1
isoband 0.2.7
iterators 1.0.14
jpeg 0.1-10
jquerylib 0.1.4
jsonlite 1.8.7
KEGGREST 1.40.1
KernSmooth 2.23-22
knitr 1.44
labeling 0.4.3
lambda.r 1.2.4
later 1.3.1
lattice 0.21-9
latticeExtra 0.6-30
lazyeval 0.2.2
leiden 0.4.3
lifecycle 1.0.3
limma 3.56.2
listenv 0.9.0
lmtest 0.9-40
locfit 1.5-9.8
lubridate 1.9.3
magrittr 2.0.3
MASS 7.3-60
Matrix 1.6-1.1
MatrixGenerics 1.12.3
MatrixModels 0.5-2
matrixStats 1.0.0
memoise 2.0.1
metapod 1.8.0
methods 4.3.1
mgcv 1.9-0
mime 0.12
miniUI 0.1.1.1
minqa 1.2.6
modelr 0.1.11
munsell 0.5.0
nlme 3.1-163
nnet 7.3-19
numDeriv 2016.8-1.1
openssl 2.1.1
operator.tools 1.6.3
ordinal 2022.11-16
pan 1.9
parallel 4.3.1
parallelly 1.36.0
patchwork 1.1.3
pbapply 1.7-2
pbdZMQ 0.3-10
pillar 1.9.0
pkgbuild 1.4.2
pkgconfig 2.0.3
pkgdown 2.0.7
pkgload 1.3.3
plogr 0.2.0
plotly 4.10.2
plyr 1.8.9
png 0.1-8
polyclip 1.10-6
praise 1.0.0
prettyunits 1.2.0
processx 3.8.2
profvis 0.3.8
progress 1.2.2
progressr 0.14.0
promises 1.2.1
ProtGenerics 1.32.0
ps 1.7.5
purrr 1.0.2
quantreg 5.97
quantsmooth 1.66.0
R6 2.5.1
ragg 1.2.5
RANN 2.6.1
rapiclient 0.1.3
rapidjsonr 1.2.0
rappdirs 0.3.3
rcmdcheck 1.4.0
RColorBrewer 1.1-3
Rcpp 1.0.11
RcppAnnoy 0.0.21
RcppArmadillo 0.12.6.4.0
RcppEigen 0.3.3.9.3
RcppHNSW 0.5.0
RcppParallel 5.1.7
RcppProgress 0.4.2
RcppTOML 0.2.2
Rcurl 1.98-1.12
readr 2.1.4
readxl 1.4.3
rematch 2.0.0
rematch2 2.1.2
remotes 2.4.2.1
repr 1.1.6
reprex 2.0.2
reshape2 1.4.4
restfulr 0.0.15
reticulate 1.32.0
Rhtslib 2.2.0
rjson 0.2.21
rlang 1.1.1
rmarkdown 2.25
ROCR 1.0-11
Ronaldo 0.1.0
roxygen2 7.2.3
rpart 4.1.19
rprojroot 2.0.3
Rsamtools 2.16.0
RSQLite 2.3.1
rstudioapi 0.15.0
rsvd 1.0.5
rtracklayer 1.60.1
Rtsne 0.16
rversions 2.1.2
rvest 1.0.3
S4Arrays 1.0.6
S4Vectors 0.38.2
SAIGEgds 2.0.1
sandwich 3.0-2
sass 0.4.7
ScaledMatrix 1.8.1
scales 1.2.1
scattermore 1.2
scran 1.28.2
scRNAseq 2.14.0
sctransform 0.4.0
scuttle 1.10.2
selectr 0.4-2
SeqArray 1.40.1
sessioninfo 1.2.2
Seurat 4.4.0
SeuratObject 4.1.4
shape 1.4.6
shiny 1.7.5
ShortRead 1.58.0
SingleCellExperiment 1.22.0
sitmo 2.0.2
skimr 2.1.5
snow 0.4-4
SNPRelate 1.34.1
sourcetools 0.1.7-1
sp 2.1-0
SparseM 1.81
sparseMatrixStats 1.12.2
spatial 7.3-17
spatstat.data 3.0-1
spatstat.explore 3.2-3
spatstat.geom 3.2-5
spatstat.random 3.1-6
spatstat.sparse 3.0-2
spatstat.utils 3.0-3
splines 4.3.1
statmod 1.5.0
stats 4.3.1
stats4 4.3.1
stringi 1.7.12
stringr 1.5.0
SummarizedExperiment 1.30.2
survival 3.5-7
sys 3.4.2
systemfonts 1.0.4
tcltk 4.3.1
tensor 1.5
testthat 3.1.10
textshaping 0.3.6
tibble 3.2.1
tidyr 1.3.0
tidyselect 1.2.0
tidyverse 2.0.0
timechange 0.2.0
tinytex 0.47
tools 4.3.1
tzdb 0.4.0
ucminf 1.2.0
urlchecker 1.0.1
usethis 2.2.2
utf8 1.2.3
utils 4.3.1
uuid 1.1-1
uwot 0.1.16
vctrs 0.6.3
viridis 0.6.4
viridisLite 0.4.2
vroom 1.6.4
waldo 0.5.1
whisker 0.4.1
withr 2.5.1
xfun 0.40
XML 3.99-0.14
xml2 1.3.5
xopen 1.0.0
xtable 1.8-4
Xvector 0.40.0
yaml 2.3.7
zip 2.3.0
zlibbioc 1.46.0
zoo 1.8-12

 

Command line tools (compgen-c)

2to3-2.7
ace2sam
aclocal
aclocal-1.16
acyclic
add-apt-repository
addr2line
afm2pl
afm2tfm
aleph
animate
animate-im6
animate-im6.q16
anthoscli
apropos
apt-add-repository
apt-extracttemplates
apt-ftparchive
apt-sortpkgs
ar
as
autoconf
autoheader
autom4te
automake
automake-1.16
autoreconf
autoscan
autosp
autoupdate
axohelp
bcomps
bdftopcf
bdftruncate
bgzip
biber
bibtex
bibtex.original
bibtex8
bibtexu
blast2sam.pl
bootctl
bowtie2sam.pl
bq
browse
bsd-from
bsd-write
bugpoint
bugpoint-10
busctl
c_rehash
c++
c++filt
c89
c89-gcc
c99
c99-gcc
cal
calendar
catman
cautious-launcher
cc
ccomps
chardet3
chardetect3
checkinstall
chkdvifont
circo
cli
cli-gacutil
cluster
col
colcrt
colrm
column
compare
compare-im6
compare-im6.q16
compile_et
compose
composite
composite-im6
composite-im6.q16
config_data
conjure
conjure-im6
conjure-im6.q16
convert
convert-im6
convert-im6.q16
corelist
cpan
cpan5.30-x86_64-linux-gnu
cpp
cpp-9
ctags
ctags.emacs
ctangle
ctie
ctwill
ctwill-refsort
ctwill-twinx
curl
curl-config
cvtsudoers
cweave
dap-config
dbilogstrip
dbiprof
dbiproxy
dbus-cleanup-sockets
dbus-daemon
dbus-monitor
dbus-run-session
dbus-send
dbus-update-activation-environment
dbus-uuidgen
derb
detex
devnag
dh_autotools-dev_restoreconfig
dh_autotools-dev_updateconfig
dh_dkms
dh_installtex
dh_perl_dbi
dh_perl_openssl
dh_python2
dialog
diffimg
dijkstra
dirmngr
dirmngr-client
disdvi
display
display-im6
display-im6.q16
docker-credential-gcloud
dot
dot_builtins
dot2gxl
dotty
dpkg-architecture
dpkg-buildflags
dpkg-buildpackage
dpkg-checkbuilddeps
dpkg-distaddfile
dpkg-genbuildinfo
dpkg-genchanges
dpkg-gencontrol
dpkg-gensymbols
dpkg-mergechangelogs
dpkg-name
dpkg-parsechangelog
dpkg-scanpackages
dpkg-scansources
dpkg-shlibdeps
dpkg-source
dpkg-vendor
dsymutil
dsymutil-10
dt2dv
dumpsexp
dv2dt
dvi2tty
dvibook
dviconcat
dvicopy
dvihp
dvilj
dvilj2p
dvilj4
dvilj4l
dvilj6
dvilualatex
dviluatex
dvipdfm
dvipdfmx
dvipdft
dvipos
dvips
dviselect
dvispc
dvitodvi
dvitomp
dvitype
dwp
ebb
ebrowse
ebrowse.emacs
edgepaint
edit
editor
elfedit
emacs
emacsclient
emacsclient.emacs
emacs-gtk
enc2xs
encguess
eptex
eqn
etags
etags.emacs
etex
euptex
ex
export2sam.pl
extractbb
f77
f95
fc-cache
fc-cat
fc-conflist
fc-list
fc-match
fc-pattern
fc-query
fc-scan
fc-validate
fdp
fftwf-wisdom
fftwl-wisdom
fftwq-wisdom
fftw-wisdom
fftw-wisdom-to-conf
file
findrule
fmtutil
fmtutil-sys
fmtutil-user
fonttosfnt
from
funzip
fusermount
g++
g++-9
gacutil
gapplication
gatk
gc
gcc
gcc-9
gcc-ar
gcc-ar-9
gcc-nm
gcc-nm-9
gcc-ranlib
gcc-ranlib-9
gcloud
gcloud-crc32c
gcov
gcov-9
gcov-dump
gcov-dump-9
gcov-tool
gcov-tool-9
gcsfuse
gdal-config
gdbus
gdbus-codegen
gdk-pixbuf-csource
gdk-pixbuf-pixdata
gdk-pixbuf-thumbnailer
genbrk
gencfu
gencnval
gendict
genrb
geos-config
geqn
GET
gfortran
gfortran-9
gftodvi
gftopk
gftype
ggobi
ginstall-info
gio
gio-querymodules
git
git-credential-gcloud.sh
git-lfs
git-receive-pack
git-shell
git-upload-archive
git-upload-pack
glib-compile-resources
glib-compile-schemas
glib-genmarshal
glib-gettextize
glib-mkenums
gml2gv
gobject-query
gold
gpg
gpg2
gpg-agent
gpgcompose
gpgconf
gpg-connect-agent
gpg-error-config
gpgparsemail
gpgrt-config
gpgsm
gpgsplit
gpgtar
gpg-wks-server
gpg-zip
gpic
gprof
graphml2gv
gregorio
grep-aptavail
grep-available
grep-dctrl
grep-debtags
grep-status
gresource
groff
grog
grops
grotty
gsettings
gsftopk
gsl-config
gsutil
gtbl
gtester
gtester-report
gtk-builder-convert
gtk-update-icon-cache
gv2gml
gv2gxl
gvcolor
gvgen
gvmap
gvmap.sh
gvpack
gvpr
gxl2dot
gxl2gv
h2ph
h2xs
h5c++
h5cc
h5fc
hd
HEAD
helpztags
hexdump
hmac256
hostnamectl
htop
htsfile
icuinfo
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ifnames
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initex
inotifywait
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ld.gold
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llvm-bcanalyzer
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llvm-cxxmap-10
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llvm-dis-10
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llvm-elfabi-10
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llvm-extract
llvm-extract-10
llvm-ifs-10
llvm-install-name-tool-10
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llvm-ranlib-10
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whatis
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wofm2opl
wopl2ofm
wovf2ovp
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x86_64-pc-linux-gnu-pkg-config
xauth
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xxd
xz
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xzless
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yaml2obj
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zip
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