Pre-configured Environment

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.

Figure 8. 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