Polly supports various notebook environments in the form of dockers to cater to the needs of different users. Each of the dockers is built according to various data analytic needs ranging from basic scripting, processing large data or training and testing of ML models. The menu to select the notebook environments will pop-up whenever you create or upload the notebook and opens it for the first time.

Menu to select various available environments

Figure 7. Menu to select various available environments

The various notebook environments supported are as follows:

Environment Usage R libraries Python Modules System
R General R scripting
  • askpass 1.1
  • assertthat 0.2.1
  • backports 1.1.5
  • base64enc 0.1-3
  • BH 1.72.0-3
  • BiocManager 1.30.10
  • bitops 1.0-6
  • brew 1.0-6
  • callr 3.4.2
  • cli 2.0.2
  • clipr 0.7.0
  • clisymbols 1.2.0
  • colorspace 1.4-1
  • commonmark 1.7
  • covr 3.4.0
  • crayon 1.3.4
  • crosstalk 1.0.0
  • curl 4.3
  • cyclocomp 1.1.0
  • desc 1.2.0
  • devtools 2.2.2
  • diffobj 0.2.3
  • digest 0.6.25
  • DT 0.12
  • ellipsis 0.3.0
  • evaluate 0.14
  • fansi 0.4.1
  • farver 2.0.3
  • fastmap 1.0.1
  • foghorn 1.1.4
  • fs 1.3.1
  • gargle 0.4.0
  • ggplot2 3.2.1
  • gh 1.1.0
  • git2r 0.26.1
  • glue 1.3.1
  • gmailr 1.0.0
  • gridExtra 2.3
  • gtable 0.3.0
  • highlight 0.5.0
  • highr 0.8
  • htmltools 0.4.0
  • htmlwidgets 1.5.1
  • httpuv 1.5.2
  • httr 1.4.1
  • hunspell 3.0
  • ini 0.3.1
  • IRdisplay 0.7.0
  • IRkernel 1.1
  • jsonlite 1.6.1
  • knitr 1.28
  • labeling 0.3
  • later 1.0.0
  • lazyeval 0.2.2
  • leaflet 2.0.3
  • leaflet.providers 1.9.0
  • lifecycle 0.1.0
  • lintr 2.0.1
  • magrittr 1.5
  • markdown 1.1
  • memoise 1.1.0
  • mime 0.9
  • mockery 0.4.2
  • munsell 0.5.0
  • openssl 1.4.1
  • parsedate 1.2.0
  • pbdZMQ 0.3-3
  • pillar 1.4.3
  • pingr 2.0.0
  • pkgbuild 1.0.6
  • pkgconfig 2.0.3
  • pkgdown 1.4.1
  • pkgload 1.0.2
  • plyr 1.8.6
  • png 0.1-7
  • PollyConnector 0.0.0
  • praise 1.0.0
  • prettyunits 1.1.1
  • processx 3.4.2
  • promises 1.1.0
  • ps 1.3.2
  • purrr 0.3.3
  • R6 2.4.1
  • rappdirs 0.3.1
  • raster 3.0-12
  • rcmdcheck 1.3.3
  • RColorBrewer 1.1-2
  • Rcpp 1.0.3
  • rematch 1.0.1
  • rematch2 2.1.0
  • remotes 2.1.1
  • repr 1.1.0
  • reshape2 1.4.3
  • reticulate 1.14
  • rex 1.1.2
  • rhub 1.1.1
  • RJSONIO 1.3-1.4
  • rlang 0.4.5
  • rmarkdown 2.1
  • roxygen2 7.0.2
  • rprojroot 1.3-2
  • rstudioapi 0.11
  • rversions 2.0.1
  • rvest 0.3.5
  • scales 1.1.0
  • selectr 0.4-2
  • sessioninfo 1.1.1
  • shiny 1.4.0
  • sourcetools 0.1.7
  • sp 1.4-1
  • spelling 2.1
  • stringi 1.4.6
  • stringr 1.4.0
  • sys 3.3
  • testthat 2.3.2
  • tibble 2.1.3
  • tinytex 0.20
  • triebeard 0.3.0
  • urltools 1.7.3
  • usethis 1.5.1
  • utf8 1.1.4
  • uuid 0.1-4
  • vctrs 0.2.3
  • viridis 0.5.1
  • viridisLite 0.3.0
  • whisker 0.4
  • whoami 1.3.0
  • withr 2.1.2
  • xfun 0.12
  • xml2 1.2.2
  • xmlparsedata 1.0.3
  • xopen 1.0.0
  • xtable 1.8-4
  • yaml 2.2.1
    None
    Python 2 General Python 2 scripting None
    • attrs 19.3.0
    • backports-abc 0.5
    • backports.functools-lru-cache 1.6.1
    • backports.shutil-get-terminal-size 1.0.0
    • bleach 3.1.0
    • certifi 2019.11.28
    • chardet 3.0.4
    • cmapPy 1.0.5
    • configparser 4.0.2
    • contextlib2 0.6.0.post1
    • cycler 0.10.0
    • decorator 4.4.1
    • defusedxml 0.6.0
    • entrypoints 0.3
    • enum34 1.1.6
    • funcsigs 1.0.2
    • functools32 3.2.3.post2
    • futures 3.3.0
    • h5py 2.10.0
    • idna 2.8
    • importlib-metadata 1.5.0
    • ipaddress 1.0.23
    • ipykernel 4.10.1
    • ipython 5.9.0
    • ipython-genutils 0.2.0
    • ipywidgets 7.4.2
    • Jinja2 2.11.1
    • jsonschema 3.2.0
    • jupyter-client 5.3.4
    • jupyter-core 4.6.2
    • kiwisolver 1.1.0
    • MarkupSafe 1.1.1
    • matplotlib 2.2.4
    • mistune 0.8.4
    • nbconvert 5.6.1
    • nbformat 4.4.0
    • notebook 5.7.8
    • numpy 1.16.6
    • pandas 0.24.1
    • pandocfilters 1.4.2
    • pathlib2 2.3.5
    • pexpect 4.8.0
    • pickleshare 0.7.5
    • plotly 3.7.0
    • prometheus-client 0.7.1
    • prompt-toolkit 1.0.18
    • ptyprocess 0.6.0
    • PubChemPy 1.0.4
    • Pygments 2.5.2
    • pyparsing 2.4.6
    • pyrsistent 0.15.7
    • python-dateutil 2.8.1
    • pytz 2019.3
    • pyzmq 18.1.1
    • qgrid 1.1.1
    • requests 2.21.0
    • retrying 1.3.3
    • scandir 1.10.0
    • scikit-learn 0.20.3
    • scipy 1.2.3
    • Send2Trash 1.5.0
    • simplegeneric 0.8.1
    • singledispatch 3.4.0.3
    • six 1.14.0
    • subprocess32 3.5.4
    • terminado 0.8.3
    • testpath 0.4.4
    • tornado 5.1.1
    • traitlets 4.3.3
    • urllib3 1.24.3
    • wcwidth 0.1.8
    • webencodings 0.5.1
    • widgetsnbextension 3.4.2
    • zipp 1.1.0
      Python 3 General Python 3 scripting None
      • alembic 1.4.1
      • async-generator 1.10
      • attrs 19.3.0
      • awscli 1.17.12
      • backcall 0.1.0
      • bleach 3.1.1
      • botocore 1.14.12
      • certifi 2019.11.28
      • chardet 3.0.4
      • colorama 0.4.3
      • cycler 0.10.0
      • decorator 4.4.2
      • defusedxml 0.6.0
      • docutils 0.15.2
      • entrypoints 0.3
      • idna 2.8
      • importlib-metadata 1.5.0
      • ipykernel 5.1.4
      • ipython 7.13.0
      • ipython-genutils 0.2.0
      • ipywidgets 7.5.1
      • jedi 0.16.0
      • Jinja2 2.11.1
      • jmespath 0.9.5
      • jsonschema 3.2.0
      • jupyter-client 6.0.0
      • jupyter-core 4.6.3
      • jupyter-dashboards 0.7.0
      • jupyterhub 0.9.4
      • kiwisolver 1.1.0
      • Mako 1.1.2
      • MarkupSafe 1.1.1
      • matplotlib 2.2.3
      • mistune 0.8.4
      • nbconvert 5.6.1
      • nbformat 5.0.4
      • notebook 5.7.2
      • numpy 1.18.1
      • pamela 1.0.0
      • pandas 1.0.1
      • pandocfilters 1.4.2
      • parso 0.6.2
      • pexpect 4.8.0
      • pickleshare 0.7.5
      • prometheus-client 0.7.1
      • prompt-toolkit 3.0.3
      • ptyprocess 0.6.0
      • pyasn1 0.4.8
      • Pygments 2.5.2
      • pyparsing 2.4.6
      • pyrsistent 0.15.7
      • python-dateutil 2.8.1
      • python-editor 1.0.4
      • python-oauth2 1.1.1
      • pytz 2019.3
      • PyYAML 5.3
      • pyzmq 19.0.0
      • qgrid 1.3.0
      • requests 2.21.0
      • rsa 3.4.2
      • s3transfer 0.3.3
      • Send2Trash 1.5.0
      • six 1.14.0
      • SQLAlchemy 1.3.13
      • terminado 0.8.3
      • testpath 0.4.4
      • tornado 5.1.1
      • traitlets 4.3.3
      • urllib3 1.24.3
      • wcwidth 0.1.8
      • webencodings 0.5.1
      • widgetsnbextension 3.5.1
      • zipp 3.1.0
        Pollyglot Multiple kernels (R, python and bash) in same notebook/environment
        • All libraries from base R docker
        • Seurat
        • pagoda2
        • CellRanger
        • SingleR
          • All libraries from base python docker
          • scanPy
          • velocyto
          • scVI(scVI supports pytorch)
          • louvain
            Barcoded Bulk RNA-seq Alignment and processing of RNA-seq fastq files with barcodes
            • All libraries from R docker
            • limma
            • affy
            • DESeq2
            • edgeR
            • cqn
            • sva
            • BioMart
            • mygene
            • amritr
            • Boruta
            • fgsea
            • gsva
            • ReactomePA
            • xCell
            • singleR
            • enrichR
            • org.Hs.eg.db
            • org.Mm.eg.db
            • Annotation dbi
            • clusterProfiler
              
              • STARsubread-1.6.4-source
              • gosaamer
              • Fastqc
              • Multiqc
              • Picard
                Machine Learning in python Training, testing and validation of ML models None
                • All libraries from base python docker
                • h5py
                • keras
                • lightgbm
                • tensorflow
                • xgboost
                  Single Cell Downstream Single Cell Analysis
                  • All libraries from base R docker
                  • Seurat
                  • pagoda2
                  • CellRanger
                  • SingleR
                  • ExperimentHub
                    • All libraries from base python docker
                    • scanPy
                    • velocyto
                    • scVI(scVI supports pytorch)
                    • louvain
                    • rpy2
                    • anndata2ri
                      Data Exploration R and python for general data analysis All libraries from base R docker All libraries from base python docker
                      RNA-seq Downstream Transcriptomics Analysis
                      • All libraries from R docker
                      • limma
                      • affy
                      • DESeq2
                      • edgeR
                      • cqn
                      • sva
                      • BioMart
                      • mygene
                      • amritr
                      • Boruta
                      • fgsea
                      • gsva
                      • ReactomePA
                      • xCell
                      • singleR
                      • enrichR
                      • org.Hs.eg.db
                      • org.Mm.eg.db
                      • Annotation dbi
                      • clusterProfiler
                        All libraries from base python docker
                        Metabolomics Metabolomics Analysis
                        • CAMERA
                        • XCMS
                        • limma
                        • matrixStats
                        • stats
                        • stringr
                        • ggplot2
                        • plotly
                        • ggsci
                        • latex2exp
                        • dplyr
                        • ggrepel
                        • SuperExactTest
                        • UpSetR
                        • PollyCommonR
                        • mapGCT
                        • MetaboAnalystR
                        • KEGGREST
                        • Pathview
                        • KEGGgraph
                        • Morpheus
                        • Pca3d
                        • X13CMS
                        • Phantasus
                        • MSnbase
                        • MAIT
                        • cmapR
                        • xMSannotator
                          All libraries from base python docker