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 |
|