- Updated jaxlib to 0.3.7 in the
scvi-scgen-scmomat-unitveloenvironment to fix an installation issue (#13) - Added doubletdetection in the
scvi-scgen-scmomat-unitveloenvironment - Fixed an installation issue of velocyto-R
- Added GEMLI
- Added DIRECT-NET
- Added scplotter
- Added parallel-fastq-dump
- Updated rapids_singlecell from 0.10.2 to 0.10.10
- Updated SRA Toolkit from 3.0.10 to v3.1.1
- Removed
MeSH.Hsa.eg.dbbecause it is not available for Bioconductor version '3.18'
- Changed Python environment from conda to micromamba (
/opt/micromamba) - Added
glmGamPoifor faster computation. - Created different flavors of ShortCake to improve usability.
- Added cell2fate
Added RENGE- Added BANKSY
- Removed monet
- Frozen ShortCake.Python (version1) Dockerfile
- Released ShortCake.Python version2 (
ShortCake_ver2) - Added CellTypist
- Added CellMap
- Fixed bug in
scvi-scgen-scmomat-unitveloConda environment by adjusting the version ofjax. - Fixed bug in
celloracleConda environment by updating the Python version from 3.7 to 3.8. - Install MS core fonts (ttf-mscorefonts-installer)
- Downgrade notebook to 6.X to change back to UI of jupyter notebook
- Fixed bug in CellRank environment: downgraded pandas to <2 to avoid "AttributeError: can't set attribute" error
- See theislab/cellrank#1078 for detail
- Added cellAlign
- Added Mowgli
- Added SCENT
- Added moslin (included in Moscot)
- Added SCOT
- Added Genes2Genes
- Added miloR
- Removed the conda environment of UniTVelo and included it in
shortcake_default
- Updated CellRank to version 2.0.0
- Added rapids_singlecell
- Created ShortCake.ver2 (Dockerfile.Python.ver2) to separate several tools of ShortCake
- Added InstaPrism
- Added the
shortcake_defaultjupyter kernel to avoid the version conflict. The tools that do not have their own kernel are included in it. - Merge several jupyter kernels
- Added STELLAR
- Added GEARS
- Added SATURN
- Added tricycle
- Added SEACells
- Added Moscot
- Added Scriabin
- Added scDesign3
- Added scReadSim
- Added CellTypist
- Added LIANA and LIANA-py
- Added RENGE
- Added MultiVelo
- Remove /root/.cpanm/work directory
- Bug fix: issue #8
- Update Seurat to v5
- Added EEISP
- Added
run_env.shto activate virtual environments in Python - Several bug fixes for installation
- Separate Seurat-related tools from Dockerfile.R (now Dockerfile.Seurat)
- Added
wget.shto download SeuratData for Docker building
- Modify bedtools files from the static binary file to ones compiled from the source
- Move Changelog to
ChangeLog.md
- Added bedtools version 2.30.0
- move scripts (jupyternotebook.sh etc) to /opt/scripts folder
- Added ikarus
- Added scTriangulate
- Added DropletQC
- Added Dictys
- Added AutoGeneS
- Added BayesPrism
- Added SignatuR
- Added scMoMaT
- Added MARIO
- Downgrade jinja2 to v3.0.3 to avoid the error in html conversion in Jupyter notebook (see issue #6).
- Added CellOracle, RECODE and JASPAR2022
- Bug fix to remove a warning "/opt/conda/lib/libtinfo.so.6: no version information available"
- Rename to ShortCake (version 1.0.0)
- Create separate environments for python tools to avoid version conflict. They can be executed from Jupyter notebook
- Separate Dockerfile to Dockerfile.R and Dockerfile.Python
- change base image from
pytorch-1.5-cuda10.1-cudnn7-develtonvidia/cuda:11.5.1-cudnn8-devel-ubuntu20.04to upgrade Python to 3.9 - Added CellChat, dyngen, Dynamo
- Added datasets in SeuratData
- Added Pagoda2
- Added programs
- Use pip venv for several tools to avoid package conflicts (e.g., tensorflow)
- Added
docker-compose.ymlto allow GitHub Token - Omit the password to login Jupyter notebook
- Added programs
- Fix several bugs in the installation
- add programs
- change base image from
Ubuntu18.04topytorch-1.5-cuda10.1-cudnn7-develto allow GPU computing
- change base image
jupyter/datascience-notebooktoUbuntu18.04