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Pre-installed tools on Researcher Workbench

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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)

R packages (installed.packages())

Command line tools (compgen -c)

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                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
absl-py                   1.0.0              pyhd8ed1ab_0    conda-forge
aiohttp                   3.8.1            py37h5e8e339_0    conda-forge
aiohttp-session           2.12.0                   pypi_0    pypi
aiosignal                 1.2.0              pyhd8ed1ab_0    conda-forge
ansiwrap                  0.8.4                      py_0    conda-forge
anyio                     3.5.0            py37h89c1867_0    conda-forge
apache-beam               2.36.0                   pypi_0    pypi
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argcomplete               2.0.0                    pypi_0    pypi
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py37h5e8e339_1    conda-forge
arrow                     1.2.2              pyhd8ed1ab_0    conda-forge
arviz                     0.12.1                   pypi_0    pypi
asn1crypto                1.4.0              pyh9f0ad1d_0    conda-forge
astroid                   2.11.6                   pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
asyncinit                 0.2.4                    pypi_0    pypi
asynctest                 0.13.0                     py_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
avro                      1.11.1                   pypi_0    pypi
azure-core                1.26.1                   pypi_0    pypi
azure-identity            1.12.0                   pypi_0    pypi
azure-storage-blob        12.14.1                  pypi_0    pypi
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bagit                     1.8.1                    pypi_0    pypi
beatrix-jupyterlab        3.1.7                    pypi_0    pypi
beautifulsoup4            4.11.1                   pypi_0    pypi
bgenix                    1.1.4                hfa204df_8    conda-forge
bgzip                     0.3.5                    pypi_0    pypi
binaryornot               0.4.4                      py_1    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                hf3e587d_10    conda-forge
biopython                 1.80                     pypi_0    pypi
black                     22.1.0             pyhd8ed1ab_0    conda-forge
bleach                    5.0.1                    pypi_0    pypi
blinker                   1.4                        py_1    conda-forge
bokeh                     1.4.0                    pypi_0    pypi
boost-cpp                 1.74.0               h312852a_4    conda-forge
boto3                     1.26.31                  pypi_0    pypi
botocore                  1.29.31                  pypi_0    pypi
bottleneck                1.3.5                    pypi_0    pypi
brewer2mpl                1.4.1                    pypi_0    pypi
brotli                    1.0.9                h7f98852_6    conda-forge
brotli-bin                1.0.9                h7f98852_6    conda-forge
brotlipy                  0.7.0           py37h27cfd23_1003  
bwidget                   1.9.14               ha770c72_1    conda-forge
bx-python                 0.9.0                    pypi_0    pypi
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cachecontrol              0.12.11                  pypi_0    pypi
cached-property           1.5.2                    pypi_0    pypi
cachetools                5.0.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
certifi                   2022.12.7                pypi_0    pypi
cffi                      1.15.0           py37h036bc23_0    conda-forge
cftime                    1.6.2                    pypi_0    pypi
chardet                   4.0.0           py37h06a4308_1003  
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
cli-builder               0.1.5                    pypi_0    pypi
click                     8.0.4            py37h89c1867_0    conda-forge
cloudpickle               2.0.0              pyhd8ed1ab_0    conda-forge
cmake                     3.22.2                   pypi_0    pypi
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
coloredlogs               15.0.1                   pypi_0    pypi
commonmark                0.9.1                    pypi_0    pypi
conda                     22.9.0           py37h89c1867_1    conda-forge
conda-package-handling    1.7.3            py37h27cfd23_1  
cookiecutter              1.7.3              pyh6c4a22f_1    conda-forge
crcmod                    1.7                      pypi_0    pypi
cromshell                 2.0.0                    pypi_0    pypi
cryptography              36.0.1           py37hf1a17b8_0    conda-forge
curl                      7.83.1               h7bff187_0    conda-forge
cwl-upgrader              1.2.4                    pypi_0    pypi
cwl-utils                 0.21                     pypi_0    pypi
cwltool                   3.1.20221201130942          pypi_0    pypi
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.32                  pypi_0    pypi
daal                      2021.6.0                 pypi_0    pypi
daal4py                   2021.6.3                 pypi_0    pypi
dataclasses               0.8                pyhc8e2a94_3    conda-forge
db-dtypes                 1.0.5                    pypi_0    pypi
debugpy                   1.5.1            py37hcd2ae1e_0    conda-forge
decorator                 4.4.2                    pypi_0    pypi
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecat                  2.1.1                    pypi_0    pypi
deprecated                1.2.13                   pypi_0    pypi
descartes                 1.1.0                    pypi_0    pypi
dill                      0.3.6                    pypi_0    pypi
dlenv-base                1.0.20220226     py37hef38c82_0    file:///tmp/conda
dlenv-tf-2-7-gpu          1.0.20220226     py37h9fc6d97_0    file:///tmp/conda
dm-tree                   0.1.6                    pypi_0    pypi
docker-py                 5.0.3            py37h89c1867_2    conda-forge
docker-pycreds            0.4.0                      py_0    conda-forge
docopt                    0.6.2                    pypi_0    pypi
dsub                      0.4.7                    pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
explainable-ai-sdk        1.3.3                    pypi_0    pypi
explainers                0.1                      pypi_0    pypi
fastavro                  1.4.9                    pypi_0    pypi
fasteners                 0.17.3                   pypi_0    pypi
fastinterval              0.1.1                    pypi_0    pypi
fastprogress              1.0.3                    pypi_0    pypi
filelock                  3.8.2                    pypi_0    pypi
firecloud                 0.16.31                  pypi_0    pypi
flatbuffers               2.0                      pypi_0    pypi
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.96              ha180cfb_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.29.1           py37h5e8e339_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
frozenlist                1.3.3                    pypi_0    pypi
fsspec                    2022.2.0           pyhd8ed1ab_0    conda-forge
funcsigs                  1.0.2                    pypi_0    pypi
future                    0.18.2                   pypi_0    pypi
gast                      0.4.0                    pypi_0    pypi
gatkpythonpackages        0.1                      pypi_0    pypi
gcc_impl_linux-64         9.5.0               h6c5bc03_17    conda-forge
gcc_linux-64              9.5.0               h4258300_10    conda-forge
gcsfs                     2022.2.0           pyhd8ed1ab_0    conda-forge
getm                      0.0.4                    pypi_0    pypi
gettext                   0.19.8.1          h73d1719_1008    conda-forge
gfortran_impl_linux-64    9.5.0               hf1096a2_19    conda-forge
gfortran_linux-64         9.5.0               hdb51d14_10    conda-forge
ggplot                    0.11.5                   pypi_0    pypi
giflib                    5.2.1                h36c2ea0_2    conda-forge
gitdb                     4.0.9              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.27             pyhd8ed1ab_0    conda-forge
gnomad                    0.6.4                    pypi_0    pypi
google-api-core           2.7.3                    pypi_0    pypi
google-api-core-grpcio-gcp 2.5.0                hd8ed1ab_0    conda-forge
google-api-python-client  2.38.0             pyhd8ed1ab_0    conda-forge
google-apitools           0.5.31                   pypi_0    pypi
google-auth               2.14.1                   pypi_0    pypi
google-auth-httplib2      0.1.0              pyhd8ed1ab_0    conda-forge
google-auth-oauthlib      0.4.6              pyhd8ed1ab_0    conda-forge
google-cloud-aiplatform   1.10.0                   pypi_0    pypi
google-cloud-appengine-logging 1.1.0                    pypi_0    pypi
google-cloud-audit-log    0.2.0                    pypi_0    pypi
google-cloud-bigquery     2.34.4                   pypi_0    pypi
google-cloud-bigquery-datatransfer 3.7.3                    pypi_0    pypi
google-cloud-bigquery-storage 2.12.0                   pypi_0    pypi
google-cloud-bigtable     2.5.2                    pypi_0    pypi
google-cloud-core         2.2.2              pyh6c4a22f_0    conda-forge
google-cloud-dataproc     3.3.0                    pypi_0    pypi
google-cloud-datastore    1.15.3                   pypi_0    pypi
google-cloud-dlp          3.6.0                    pypi_0    pypi
google-cloud-firestore    2.3.4                    pypi_0    pypi
google-cloud-kms          2.11.0                   pypi_0    pypi
google-cloud-language     1.3.0                    pypi_0    pypi
google-cloud-logging      3.0.0                    pypi_0    pypi
google-cloud-monitoring   2.8.0                    pypi_0    pypi
google-cloud-pubsub       2.9.0                    pypi_0    pypi
google-cloud-pubsublite   1.4.0                    pypi_0    pypi
google-cloud-recommendations-ai 0.2.0                    pypi_0    pypi
google-cloud-resource-manager 1.6.3                    pypi_0    pypi
google-cloud-scheduler    2.6.0                    pypi_0    pypi
google-cloud-spanner      3.13.0                   pypi_0    pypi
google-cloud-speech       2.12.0                   pypi_0    pypi
google-cloud-storage      1.44.0                   pypi_0    pypi
google-cloud-tasks        2.8.0                    pypi_0    pypi
google-cloud-translate    3.7.0                    pypi_0    pypi
google-cloud-videointelligence 2.6.0                    pypi_0    pypi
google-cloud-vision       1.0.0                    pypi_0    pypi
google-crc32c             1.1.2            py37hab72019_2    conda-forge
google-pasta              0.2.0                    pypi_0    pypi
google-resumable-media    2.4.0                    pypi_0    pypi
googleapis-common-protos  1.57.0                   pypi_0    pypi
graphite2                 1.3.13            h58526e2_1001    conda-forge
greenlet                  1.1.2            py37hcd2ae1e_1    conda-forge
grpc-google-iam-v1        0.12.4                   pypi_0    pypi
grpcio                    1.44.0           py37hb27c1af_0    conda-forge
grpcio-gcp                0.2.2            py37h89c1867_5    conda-forge
grpcio-status             1.44.0                   pypi_0    pypi
gs-chunked-io             0.5.2                    pypi_0    pypi
gsl                       2.7                  he838d99_0    conda-forge
gxx_impl_linux-64         9.5.0               h6c5bc03_17    conda-forge
gxx_linux-64              9.5.0               h43f449f_10    conda-forge
h5py                      3.7.0                    pypi_0    pypi
hail                      0.2.107                  pypi_0    pypi
harfbuzz                  3.1.1                h83ec7ef_0    conda-forge
hdbscan                   0.8.29                   pypi_0    pypi
hdfs                      2.6.0                    pypi_0    pypi
horovod                   0.23.0                   pypi_0    pypi
html5lib                  1.1                      pypi_0    pypi
htmlmin                   0.1.12                     py_1    conda-forge
httplib2                  0.20.4             pyhd8ed1ab_0    conda-forge
humanfriendly             10.0                     pypi_0    pypi
humanize                  1.1.0                    pypi_0    pypi
hurry-filesize            0.9                      pypi_0    pypi
icu                       68.2                 h9c3ff4c_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
igv-jupyter               1.0.0                    pypi_0    pypi
imagehash                 4.2.1              pyhd8ed1ab_0    conda-forge
imageio                   2.16.0                   pypi_0    pypi
importlib-metadata        4.11.1           py37h89c1867_0    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
intel-openmp              2022.2.1                 pypi_0    pypi
ipykernel                 6.9.1            py37h6531663_0    conda-forge
ipython                   7.32.0           py37h89c1867_0    conda-forge
ipython-sql               0.3.9           pyhd8ed1ab_1004    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5                    pypi_0    pypi
isal                      1.1.0                    pypi_0    pypi
isodate                   0.6.1                    pypi_0    pypi
isort                     5.10.1                   pypi_0    pypi
janus                     1.0.0                    pypi_0    pypi
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.1           py37h89c1867_0    conda-forge
jeepney                   0.7.1                    pypi_0    pypi
jinja2                    3.0.3                    pypi_0    pypi
jinja2-time               0.2.0                      py_2    conda-forge
jmespath                  0.10.0                   pypi_0    pypi
joblib                    1.2.0                    pypi_0    pypi
jpeg                      9e                   h7f98852_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.4.0              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0                    pypi_0    pypi
jupyter-console           6.4.0                    pypi_0    pypi
jupyter-contrib-core      0.3.3                    pypi_0    pypi
jupyter-contrib-nbextensions 0.5.1                    pypi_0    pypi
jupyter-highlight-selected-word 0.2.0                    pypi_0    pypi
jupyter-http-over-ws      0.0.8                    pypi_0    pypi
jupyter-latex-envs        1.4.6                    pypi_0    pypi
jupyter-nbextensions-configurator 0.4.1                    pypi_0    pypi
jupyter-server-mathjax    0.2.5              pyhc268e32_0    conda-forge
jupyter-server-proxy      3.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.2            py37h89c1867_0    conda-forge
jupyter_server            1.13.5             pyhd8ed1ab_1    conda-forge
jupyterlab                3.2.9              pyhd8ed1ab_0    conda-forge
jupyterlab-git            0.34.2             pyhd8ed1ab_0    conda-forge
jupyterlab-widgets        1.0.2                    pypi_0    pypi
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.10.3             pyhd8ed1ab_0    conda-forge
jupytext                  1.13.7             pyhd0ecf6b_0    conda-forge
keras                     2.7.0                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
keras-tuner               1.1.0                    pypi_0    pypi
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyring                   23.5.0                   pypi_0    pypi
keyrings-google-artifactregistry-auth 1.0.0                    pypi_0    pypi
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.3.2            py37h2527ec5_1    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
kt-legacy                 1.0.4                    pypi_0    pypi
lazy-object-proxy         1.7.1                    pypi_0    pypi
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           13_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h7f98852_6    conda-forge
libbrotlidec              1.0.9                h7f98852_6    conda-forge
libbrotlienc              1.0.9                h7f98852_6    conda-forge
libcblas                  3.9.0           13_linux64_openblas    conda-forge
libclang                  13.0.0                   pypi_0    pypi
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   7.83.1               h7bff187_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     9.5.0               h367e8d2_17    conda-forge
libgcc-ng                 11.2.0              h1d223b6_12    conda-forge
libgfortran-ng            11.2.0              h69a702a_12    conda-forge
libgfortran5              11.2.0              h5c6108e_12    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   11.2.0              h1d223b6_12    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           13_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_3    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libprotobuf               3.19.4               h780b84a_0    conda-forge
libsanitizer              9.5.0               hf86b28c_17    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-devel_linux-64  9.5.0               h367e8d2_17    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_12    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.42.0               h7f98852_0    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
llvmlite                  0.38.0           py37h9d7f4d0_0    conda-forge
lockfile                  0.12.2                   pypi_0    pypi
lxml                      4.9.0                    pypi_0    pypi
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
mako                      1.2.4                    pypi_0    pypi
markdown                  3.3.6              pyhd8ed1ab_0    conda-forge
markdown-it-py            1.1.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.0.1            py37h5e8e339_1    conda-forge
matplotlib-base           3.5.1            py37h1058ff1_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
matplotlib-venn           0.11.7                   pypi_0    pypi
mccabe                    0.7.0                    pypi_0    pypi
mdit-py-plugins           0.3.0              pyhd8ed1ab_0    conda-forge
missingno                 0.4.2                      py_1    conda-forge
mistune                   0.8.4           py37h5e8e339_1005    conda-forge
mizani                    0.7.3                    pypi_0    pypi
mkl                       2022.2.1                 pypi_0    pypi
mock                      4.0.3                    pypi_0    pypi
msal                      1.20.0                   pypi_0    pypi
msal-extensions           1.0.0                    pypi_0    pypi
msgpack                   1.0.4                    pypi_0    pypi
msrest                    0.7.1                    pypi_0    pypi
multidict                 6.0.2            py37h5e8e339_0    conda-forge
multimethod               1.4                        py_0    conda-forge
multiprocess              0.70.14                  pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           0.4.3            py37h89c1867_4    conda-forge
nb_conda                  2.2.1            py37h89c1867_4    conda-forge
nb_conda_kernels          2.3.1            py37h89c1867_1    conda-forge
nbclassic                 0.3.5              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.11             pyhd8ed1ab_0    conda-forge
nbconvert                 6.5.0                    pypi_0    pypi
nbdime                    3.1.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
nbstripout                0.6.1                    pypi_0    pypi
ncurses                   6.3                  h9c3ff4c_0    conda-forge
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
netcdf4                   1.6.2                    pypi_0    pypi
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
nodejs                    12.22.6              h8b53aa1_0    conda-forge
nose                      1.3.7                    pypi_0    pypi
notebook                  6.4.8              pyha770c72_0    conda-forge
notebook-executor         0.2                      pypi_0    pypi
numba                     0.55.1           py37h2d894fd_0    conda-forge
numpy                     1.21.6                   pypi_0    pypi
oauth2client              4.1.3                    pypi_0    pypi
oauthlib                  3.2.0              pyhd8ed1ab_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1o               h166bdaf_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
orjson                    3.6.7                    pypi_0    pypi
overrides                 6.1.0                    pypi_0    pypi
packaging                 21.3               pyhd8ed1ab_0    conda-forge
palettable                3.3.0                    pypi_0    pypi
pandas                    1.3.5            py37he8f5f7f_0    conda-forge
pandas-gbq                0.17.9                   pypi_0    pypi
pandas-profiling          3.0.0                    pypi_0    pypi
pandoc                    2.17.1.1             ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.48.10              h54213e6_2    conda-forge
papermill                 2.3.4              pyhd8ed1ab_0    conda-forge
parameterized             0.8.1                    pypi_0    pypi
parsimonious              0.8.1                    pypi_0    pypi
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3                    pypi_0    pypi
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
pdoc3                     0.10.0                   pypi_0    pypi
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
phik                      0.12.0           py37h18a2d16_1    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.0.1            py37h44f0d7a_2    conda-forge
pip                       22.3.1                   pypi_0    pypi
pixman                    0.40.0               h36c2ea0_0    conda-forge
platformdirs              2.5.1              pyhd8ed1ab_0    conda-forge
plotly                    5.10.0                   pypi_0    pypi
plotnine                  0.8.0                    pypi_0    pypi
pluggy                    1.0.0                    pypi_0    pypi
portalocker               2.6.0                    pypi_0    pypi
poyo                      0.5.0                      py_0    conda-forge
prettytable               3.1.1              pyhd8ed1ab_0    conda-forge
prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge
promise                   2.3                      pypi_0    pypi
prompt-toolkit            3.0.27             pyha770c72_0    conda-forge
proto-plus                1.22.1                   pypi_0    pypi
protobuf                  3.20.2                   pypi_0    pypi
prov                      1.5.1                    pypi_0    pypi
psutil                    5.9.0                    pypi_0    pypi
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulp                      2.7.0                    pypi_0    pypi
py4j                      0.10.9.7                 pypi_0    pypi
pyarrow                   7.0.0                    pypi_0    pypi
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.3            py37h27cfd23_0  
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.9.0            py37h5e8e339_0    conda-forge
pydata-google-auth        1.4.0                    pypi_0    pypi
pydot                     1.4.2                    pypi_0    pypi
pyfaidx                   0.7.1                    pypi_0    pypi
pyfasta                   0.5.2                    pypi_0    pypi
pygments                  2.12.0                   pypi_0    pypi
pyjwt                     2.3.0              pyhd8ed1ab_1    conda-forge
pylint                    1.7.2                    pypi_0    pypi
pymc3                     3.11.5                   pypi_0    pypi
pymongo                   3.12.3                   pypi_0    pypi
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pypandoc                  1.10                     pypi_0    pypi
pyparsing                 2.4.7                    pypi_0    pypi
pyrsistent                0.18.1           py37h5e8e339_0    conda-forge
pysam                     0.20.0                   pypi_0    pypi
pysocks                   1.7.1                    py37_1  
python                    3.7.12          hb7a2778_100_cpython    conda-forge
python-datauri            1.1.0                    pypi_0    pypi
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.4                    pypi_0    pypi
python-kubernetes         22.6.0             pyhd8ed1ab_0    conda-forge
python-lzo                1.14                     pypi_0    pypi
python-slugify            6.1.0              pyhd8ed1ab_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge
pytz                      2022.1                   pypi_0    pypi
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pyvcf3                    1.0.3                    pypi_0    pypi
pywavelets                1.2.0            py37hb1e94ed_1    conda-forge
pyyaml                    6.0              py37h5e8e339_3    conda-forge
pyzmq                     22.3.0           py37h336d617_1    conda-forge
qtconsole                 5.2.2                    pypi_0    pypi
r-base                    4.1.1                hb93adac_1    conda-forge
r-data.table              1.14.2            r41hcfec24a_0    conda-forge
r-docopt                  0.7.1             r41hc72bb7e_2    conda-forge
r-getopt                  1.20.3            r41ha770c72_3    conda-forge
r-lattice                 0.20_45           r41hcfec24a_0    conda-forge
r-matrix                  1.4_1             r41h0154571_0    conda-forge
r-optparse                1.7.3             r41hc72bb7e_1    conda-forge
r-qlcmatrix               0.9.7           r41hc72bb7e_1003    conda-forge
r-rcpp                    1.0.8.3           r41h7525677_0    conda-forge
r-rcppparallel            5.1.5             r41h03ef668_0    conda-forge
r-rhpcblasctl             0.21_247.1        r41hcfec24a_0    conda-forge
r-saige                   0.45.0            r41hce4ab8e_3    bioconda
r-slam                    0.1_50            r41hb699f27_1    conda-forge
r-sparsesvd               0.2               r41hcfec24a_1    conda-forge
r-spatest                 3.1.2             r41hc72bb7e_1    conda-forge
rdflib                    6.2.0                    pypi_0    pypi
readline                  8.1                  h27cfd23_0  
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
retrying                  1.3.3                    pypi_0    pypi
rich                      12.6.0                   pypi_0    pypi
rsa                       4.8                pyhd8ed1ab_0    conda-forge
ruamel-yaml               0.17.21                  pypi_0    pypi
ruamel-yaml-clib          0.2.7                    pypi_0    pypi
ruamel_yaml               0.15.100         py37h27cfd23_0  
s3transfer                0.6.0                    pypi_0    pypi
savvy                     2.0.1                hfb1f815_4    bioconda
schema-salad              8.3.20221115203138          pypi_0    pypi
scikit-image              0.19.2                   pypi_0    pypi
scikit-learn              1.0.2            py37hf9e9bfc_0    conda-forge
scikit-learn-intelex      2021.6.3                 pypi_0    pypi
scipy                     1.7.3            py37hf2a6cf1_0    conda-forge
seaborn                   0.12.1                   pypi_0    pypi
secretstorage             3.3.1                    pypi_0    pypi
sed                       4.8                  he412f7d_0    conda-forge
semver                    2.13.0                   pypi_0    pypi
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                59.8.0           py37h89c1867_0    conda-forge
shellescape               3.8.1                    pypi_0    pypi
shrinkwrap                1.2.0                h8332532_0    conda-forge
simpervisor               0.4                pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyhd3eb1b0_0  
slackclient               2.5.0                    pypi_0    pypi
smmap                     3.0.5              pyh44b312d_0    conda-forge
sniffio                   1.2.0            py37h89c1867_2    conda-forge
sortedcontainers          2.4.0                    pypi_0    pypi
soupsieve                 2.3.2.post1              pypi_0    pypi
sqlalchemy                1.4.31           py37h5e8e339_0    conda-forge
sqlite                    3.37.0               h9cd32fc_0    conda-forge
sqlparse                  0.4.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.13.5                   pypi_0    pypi
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tabulate                  0.8.9                    pypi_0    pypi
tangled-up-in-unicode     0.1.0              pyhd8ed1ab_0    conda-forge
tbb                       2021.7.1                 pypi_0    pypi
tenacity                  7.0.0                    pypi_0    pypi
tensorboard               2.8.0                    pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-wit    1.8.1                    pypi_0    pypi
tensorflow                2.7.0                    pypi_0    pypi
tensorflow-cloud          0.1.16                   pypi_0    pypi
tensorflow-datasets       4.4.0                    pypi_0    pypi
tensorflow-estimator      2.7.0                    pypi_0    pypi
tensorflow-hub            0.12.0                   pypi_0    pypi
tensorflow-io             0.23.1                   pypi_0    pypi
tensorflow-io-gcs-filesystem 0.24.0                   pypi_0    pypi
tensorflow-metadata       1.6.0                    pypi_0    pypi
tensorflow-probability    0.14.1                   pypi_0    pypi
tensorflow-serving-api    2.7.0                    pypi_0    pypi
tensorflow-transform      1.6.0                    pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
terminado                 0.13.1           py37h89c1867_0    conda-forge
terra-notebook-utils      0.9.3                    pypi_0    pypi
terra-widgets             0.0.1                    pypi_0    pypi
testpath                  0.6.0              pyhd8ed1ab_0    conda-forge
text-unidecode            1.3                        py_0    conda-forge
textwrap3                 0.9.2                      py_0    conda-forge
tfx-bsl                   1.6.0                    pypi_0    pypi
theano                    1.0.5                    pypi_0    pypi
theano-pymc               1.1.2                    pypi_0    pypi
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2021.11.2                pypi_0    pypi
tinycss2                  1.1.1                    pypi_0    pypi
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py37h5e8e339_2    conda-forge
tqdm                      4.64.1                   pypi_0    pypi
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.2            py37h5e8e339_0    conda-forge
typing-extensions         4.1.1                hd8ed1ab_0    conda-forge
typing-inspect            0.7.1                    pypi_0    pypi
typing-utils              0.1.0                    pypi_0    pypi
typing_extensions         4.1.1              pyha770c72_0    conda-forge
ujson                     5.1.0            py37hcd2ae1e_0    conda-forge
unicodedata2              14.0.0           py37h5e8e339_0    conda-forge
unidecode                 1.3.3              pyhd8ed1ab_0    conda-forge
uritemplate               4.1.1              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.8             pyhd8ed1ab_1    conda-forge
uvloop                    0.17.0                   pypi_0    pypi
visions                   0.7.1                    pypi_0    pypi
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.3.1              pyhd8ed1ab_0    conda-forge
werkzeug                  2.2.2                    pypi_0    pypi
whatshap                  1.7                      pypi_0    pypi
wheel                     0.38.4                   pypi_0    pypi
widgetsnbextension        3.5.2                    pypi_0    pypi
witwidget                 1.8.0                    pypi_0    pypi
wrapt                     1.13.3           py37h5e8e339_1    conda-forge
xai-tabular-widget        0.1.0                    pypi_0    pypi
xarray                    0.20.2                   pypi_0    pypi
xarray-einstats           0.2.2                    pypi_0    pypi
xgboost                   1.6.2                    pypi_0    pypi
xopen                     1.7.0                    pypi_0    pypi
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
yarl                      1.7.2            py37h5e8e339_1    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

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

 

R packages (installed.packages ())

Package Version
abind 1.4-5
annotate 1.76.0
AnnotationDbi 1.60.0
AnnotationFilter 1.22.0
AnnotationHub 3.6.0
AnVIL 1.10.1
askpass 1.1
assertthat 0.2.1
backports 1.4.1
base64enc 0.1-3
beachmat 2.14.0
BH 1.78.0-0
bigrquery 1.4.1
Biobase 2.58.0
BiocFileCache 2.6.0
BiocGenerics 0.44.0
BiocIO 1.8.0
BiocManager 1.30.19
BiocNeighbors 1.16.0
BiocParallel 1.32.4
BiocSingular 1.14.0
BiocVersion 3.16.0
biomaRt 2.54.0
Biostrings 2.66.0
bit 4.0.5
bit64 4.0.5
bitops 1.0-7
blob 1.2.3
bluster 1.8.0
boot 1.3-28.1
brew 1.0-8
brio 1.1.3
broom 1.0.1
bslib 0.4.1
cachem 1.0.6
callr 3.7.3
caTools 1.18.2
cellranger 1.1.0
class 7.3-20
cli 3.4.1
clipr 0.8.0
cluster 2.1.4
codetools 0.2-18
colorspace 2.0-3
commonmark 1.8.1
cowplot 1.1.1
cpp11 0.4.3
crayon 1.5.2
credentials 1.3.2
crosstalk 1.2.0
curl 4.3.3
data.table 1.14.6
DBI 1.1.3
dbplyr 2.2.1
DelayedArray 0.24.0
DelayedMatrixStats 1.20.0
deldir 1.0-6
desc 1.4.2
DESeq2 1.38.1
devtools 2.4.5
diffobj 0.3.5
digest 0.6.30
DNAcopy 1.72.2
downlit 0.4.2
dplyr 1.0.10
dqrng 0.3.0
DT 0.26
dtplyr 1.2.2
edgeR 3.40.0
ellipsis 0.3.2
ensembldb 2.22.0
evaluate 0.18
ExperimentHub 2.6.0
fansi 1.0.3
farver 2.1.1
fastmap 1.1.0
filelock 1.0.2
fitdistrplus 1.1-8
FNN 1.1.3.1
fontawesome 0.4.0
forcats 0.5.2
foreign 0.8-84
formatR 1.12
formula.tools 1.7.1
fs 1.5.2
futile.logger 1.4.3
futile.options 1.0.1
future 1.29.0
future.apply 1.10.0
gargle 1.2.1
gdsfmt 1.34.0
geneplotter 1.76.0
generics 0.1.3
GENESIS 2.28.0
GenomeInfoDb 1.34.4
GenomeInfoDbData 1.2.9
GenomicAlignments 1.34.0
GenomicFeatures 1.50.2
GenomicRanges 1.50.1
gert 1.9.2
ggplot2 3.4.0
ggrepel 0.9.2
ggridges 0.5.4
gh 1.3.1
gitcreds 0.1.2
globals 0.16.2
glue 1.6.2
goftest 1.2-3
googleAuthR 2.0.0
googleCloudStorageR 0.7.0
googledrive 2.0.0
googlesheets4 1.0.1
gplots 3.1.3
gridExtra 2.3
gtable 0.3.1
gtools 3.9.4
GWASExactHW 1.01
GWASTools 1.44.0
haven 2.5.1
here 1.0.1
highr 0.9
hms 1.1.2
htmltools 0.5.4
htmlwidgets 1.5.4
httpuv 1.6.6
httr 1.4.4
hwriter 1.3.2.1
ica 1.0-3
ids 1.0.1
igraph 1.3.5
ini 0.3.1
interactiveDisplayBase 1.36.0
interp 1.1-3
IRanges 2.32.0
IRdisplay 1.1
IRkernel 1.3.1
irlba 2.3.5.1
isoband 0.2.6
jpeg 0.1-10
jquerylib 0.1.4
jsonlite 1.8.4
KEGGREST 1.38.0
KernSmooth 2.23-20
knitr 1.41
labeling 0.4.2
lambda.r 1.2.4
later 1.3.0
lattice 0.20-45
latticeExtra 0.6-30
lazyeval 0.2.2
leiden 0.4.3
lifecycle 1.0.3
limma 3.54.0
listenv 0.8.0
lmtest 0.9-40
locfit 1.5-9.6
logistf 1.24.1
lubridate 1.9.0
magrittr 2.0.3
MASS 7.3-58.1
Matrix 1.5-3
MatrixGenerics 1.10.0
MatrixModels 0.5-1
matrixStats 0.63.0
memoise 2.0.1
metapod 1.6.0
mgcv 1.8-41
mice 3.15.0
mime 0.12
miniUI 0.1.1.1
modelr 0.1.10
munsell 0.5.0
nlme 3.1-160
nnet 7.3-18
openssl 2.0.5
operator.tools 1.6.3
parallelly 1.32.1
patchwork 1.1.2
pbapply 1.6-0
pbdZMQ 0.3-8
pillar 1.8.1
pkgbuild 1.4.0
pkgconfig 2.0.3
pkgdown 2.0.6
pkgload 1.3.2
plogr 0.2.0
plotly 4.10.1
plyr 1.8.8
png 0.1-8
polyclip 1.10-4
praise 1.0.0
prettyunits 1.1.1
processx 3.8.0
profvis 0.3.7
progress 1.2.2
progressr 0.11.0
promises 1.2.0.1
ProtGenerics 1.30.0
ps 1.7.2
purrr 0.3.5
quantreg 5.94
quantsmooth 1.64.0
R6 2.5.1
ragg 1.2.4
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 1.0.9
RcppAnnoy 0.0.20
RcppArmadillo 0.11.4.2.1
RcppEigen 0.3.3.9.3
RcppHNSW 0.4.1
RcppProgress 0.4.2
RcppTOML 0.1.7
RCurl 1.98-1.9
readr 2.1.3
readxl 1.4.1
rematch 1.0.1
rematch2 2.1.2
remotes 2.4.2
repr 1.1.4
reprex 2.0.2
reshape2 1.4.4
restfulr 0.0.15
reticulate 1.26
Rhtslib 2.0.0
rjson 0.2.21
rlang 1.0.6
rmarkdown 2.18
ROCR 1.0-11
Ronaldo 0.1.0
roxygen2 7.2.2
rpart 4.1.19
rprojroot 2.0.3
Rsamtools 2.14.0
RSQLite 2.2.19
rstudioapi 0.14
rsvd 1.0.5
rtracklayer 1.58.0
Rtsne 0.16
rversions 2.1.2
rvest 1.0.3
S4Vectors 0.36.1
sandwich 3.0-2
sass 0.4.4
ScaledMatrix 1.6.0
scales 1.2.1
scattermore 0.8
scran 1.26.0
scRNAseq 2.12.0
sctransform 0.3.5
scuttle 1.8.2
selectr 0.4-2
SeqArray 1.38.0
SeqVarTools 1.36.0
sessioninfo 1.2.2
Seurat 4.3.0
SeuratObject 4.1.3
shiny 1.7.3
ShortRead 1.56.1
SingleCellExperiment 1.20.0
sitmo 2.0.2
snow 0.4-4
SNPRelate 1.32.1
sourcetools 0.1.7
sp 1.5-1
SparseM 1.81
sparseMatrixStats 1.10.0
spatial 7.3-15
spatstat.data 3.0-0
spatstat.explore 3.0-5
spatstat.geom 3.0-3
spatstat.random 3.0-1
spatstat.sparse 3.0-0
spatstat.utils 3.0-1
statmod 1.4.37
stringi 1.7.8
stringr 1.5.0
SummarizedExperiment 1.28.0
survival 3.4-0
sys 3.4.1
systemfonts 1.0.4
tensor 1.5
testthat 3.1.5
textshaping 0.3.6
tibble 3.1.8
tidyr 1.2.1
tidyselect 1.2.0
tidyverse 1.3.2
timechange 0.1.1
tinytex 0.42
tzdb 0.3.0
urlchecker 1.0.1
usethis 2.1.6
utf8 1.2.2
uuid 1.1-0
uwot 0.1.14
vctrs 0.5.1
viridisLite 0.4.1
vroom 1.6.0
waldo 0.4.0
whisker 0.4.1
withr 2.5.0
xfun 0.35
XML 3.99-0.13
xml2 1.3.3
xopen 1.0.0
xtable 1.8-4
XVector 0.38.0
yaml 2.3.6
zip 2.2.2
zlibbioc 1.44.0
zoo 1.8-11
base 4.2.2
compiler 4.2.2
datasets 4.2.2
graphics 4.2.2
grDevices 4.2.2
grid 4.2.2
methods 4.2.2
parallel 4.2.2
splines 4.2.2
stats 4.2.2
stats4 4.2.2
tcltk 4.2.2
tools 4.2.2
utils 4.2.2

 

Command line tools (compgen-c)

lnstat
ss
nextflow
gatk
xprop
luit
clhsdb
interpolate_sam.pl
xzmore
xlsfonts
python3.7m
maq2sam-short
xev
seq_cache_populate.pl
psl2sam.pl
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