Releases: jkobject/genepy
Releases · jkobject/genepy
1.1.1
Javad Noorbakhsh (15):
import and indent issues, and missing functions
use subplots for qc metrics
minor
tighten the heatmap
automatic linter
allow tilde for home directory
Merge pull request #4 from broadinstitute/async
number of files smaller by one
map terra workflow
add tqdm
Merge pull request #10 from broadinstitute/workspace_update
add biomart
fix whitespace
add requester pays
drop duplicate file
Jérémie Kalfon (18):
removing useless modules
pypi setup finish
removing dup
updating reqs
Merge branch 'dev'
making CREME
Merge branch 'dev' of https://github.com/broadinstitute/genepy into dev
Merge remote-tracking branch 'origin/master' into dev
debugging some requirements
nothing really
adding more setups
Merge branch 'dev' of https://github.com/broadinstitute/genepy into dev
updating CREME
Merge branch 'master' into dev
adding examples
Merge branch 'dev' of https://github.com/broadinstitute/genepy into dev
improving vcf reading and cleanup
Merge branch 'master' of https://github.com/broadinstitute/genepy
Jérémie Kalfon (34):
Update README.md
Create python-publish.yml
Create python-package.yml
Create codeql-analysis.yml
Update requirements.txt
Update python-package.yml
Update requirements.txt
Update python-package.yml
Update requirements.txt
Update requirements.txt
Update requirements.txt
Merge pull request #2 from broadinstitute/cleanup-rnaseqc-plots
Merge pull request #1 from broadinstitute/dev
Merge pull request #3 from broadinstitute/rnaqc-plots
Merge pull request #6 from broadinstitute/setup-patch
Merge pull request #7 from broadinstitute/workflow-graphs
Merge pull request #11 from broadinstitute/bamdates
Update genepy/mutations/__init__.py
Update genepy/terra/__init__.py
Update genepy/terra/__init__.py
Merge pull request #12 from broadinstitute/dev
Merge branch 'master' into fix-install
Merge pull request #14 from broadinstitute/fix-install
Merge pull request #15 from monikaperez/master
Merge pull request #16 from broadinstitute/sharebams-requesterpays
Merge pull request #17 from broadinstitute/dev
Update setup.py
Update setup.py
Update helper.py
Update __init__.py
Update genepy/terra/__init__.py
Merge pull request #2 from WhiteLabGenomics/Feat-update-uploadFromFolder
Merge pull request #11 from WhiteLabGenomics/master
Update README.md
Monika Perez (2):
Update plot.py
Merge branch 'broadinstitute:master' into master
Simone Zhang (5):
add helper function to generateGeneNames
Update genepy/utils/helper.py
Update genepy/utils/helper.py
Update genepy/utils/helper.py
Merge pull request #13 from broadinstitute/edit-generateGeneNames
Xi (5):
upddate uploadFromFolder for samplesetname
update uploadFromFolder for samplesetname
Merge branch 'Feat-update-uploadFromFolder' of https://github.com/WhiteLabGenomics/genepy into Feat-update-uploadFromFolder
make samplesetname a required argument
fix: volcano render_mode and output_backend
jkobject (146):
updating paths to GenePy
new reqs
updating genepy name and adding new gcpfunction to rename folders
working on doc chipseq
moving files
readding rose
debugging
updating the readme
updating readme
updating the setup
debugging rnaseq
adding some documentation
switching to asynchronous functions and adding a new heatmap plot
little improvements and debugging
Merge branch 'dev' of https://github.com/broadinstitute/genepy into dev
some debug
updating workspace save function
debugging a plog function
working on cobinding
making a microscopy file
Merge branch 'master' of https://github.com/BroadInstitute/GenepY
making svgs
Merge commit 'b9cba418efcb0b695a98a501cb30a8cd7ba8c933' into dev
some required debugs
adding microscopy work
resetting format
Merge commit '0e0c4ba3649e786c40de80a79dd46ffd026754e0' into dev
updating superRes micrroscopy tools
some cleanup and reformating
a quick debug
WIP (nostash)
debugging an issue with th terra function
updating fish
creating a cellosaurus export
new gcp share file function (more generalistic)
more general toGeneMatric function
some debug and changing indentation
Merge branch 'dev' of https://github.com/broadinstitute/genepy into dev
debugging sheet file used
updating for new sns package
updates and debugs
adding ability to cache ssgsea
debugging some issues with dalmatian (working WIP)
import helper
adding gene name generation function
making genepy much lighter
making CCLE only function hidden
updating plots
Merge branch 'master' into dev
cleaning up indents
debugging some things
allowing to remove access
some debug
updating installation
debugging volcano plot search and pyDeSeq
indentation
slight improvements in binry mat and gsva func
reworking slightly
improving plot size
make it more productionalized
adding a website
debug a function
bettr doc
some debug
reworking website
updates and debug from Mo's pull request
release: version 0.5.0 🚀
add release message
release: version 0.5.1 🚀
release: version 0.5.2 🚀
chmod
release: version 0.5.3 🚀
release: version 0.5.4 🚀
update release
release: version 0.5.5 🚀
release: version 0.5.6 🚀
updating setup
release: version 0.5.7 🚀
updating setup
release: version 0.5.8 🚀
again
release: version 0.5.9 🚀
release: version 1.1 🚀
release: version 1.1.0 🚀
release: version 1.1.1 🚀
release: version 1.1.2 🚀
updating requirements
release: version 1.1.3 🚀
some slight debug and improvement
debug
adding some documentation
nothing really
better doc
improvement in makeCellosaurusExport
adding new function
updating CREME
Merge branch 'master' of https://github.com/BroadInstitute/GenepY
finishing dbug of CREME
adding a fifth plotting information (shape)
adding shape as plotting information
starting work on merging
Merge branch 'master' of https://github.com/BroadInstitute/GenepY
debug of plotting and indentation
adding indentation setting vscode
improvements on scatter and reformatting
adding a new unction and reformatting seq
dropping CCLE related function
reformating
adding update_entities function
debugging ssgsea and some indent
Merge branch 'master' of https://github.com/broadinstitute/genepy
reformating mutations
Merge branch 'master' into dev
debugging reading vcfs
release: version 1.2.0 🚀
debugging installing r-package
release: version 1.2.1 🚀
debug
debugging vcf_to_df more
improving the to_vcf and big plotting speedup
big plotting speedup
debugging in corner cases and adding more features
Merge remote-tracking branch 'origin/master' into dev
release: version 1.2.2 🚀
changing reqs
release: version 1.2.4 🚀
adding ability to drop cols
release: version 1.2.5 🚀
PGT
improving doc and format
improving ls
release: version 1.2.6 🚀
a couple new features, improvements and debug
release: version 1.2.7 🚀
allowing searchbox in scatter
adding documentation
adding some more doc
debug bokeh layout
Merge branch 'master' of https://github.com/WhiteLabGenomics/genepy
debug genepy on python 3.9
debug some mutations
Merge branch 'master' of https://github.com/WhiteLabGenomics/genepy
removing the long setyp
better readme
Merge remote-tracking branch 'jk-genepy/master'
better ensemble parsing
monikaperez (5):
change convertGenes to not require taiga dependency
Resolved merge conflict by adding upstream indent changes.
Removed unused imports. Removed pushed conflict.
Removed print comments in readSlamDunk.
cleaned up indents and removed unnecessary prints