shahcompbio/scgenome issues and pull requests

#87 - build(deps): bump requests from 2.28 to 2.31.0

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#86 - deleting unused code

Pull Request - State: closed - Opened by diljotgrewal 11 months ago

#85 - Fixes

Pull Request - State: closed - Opened by amcpherson 11 months ago

#84 - Creating adata can fail due to duplicated control cells

Issue - State: open - Opened by mmyers1 over 1 year ago

#83 - feature: refgenome chromosome info refactor

Pull Request - State: closed - Opened by amcpherson almost 2 years ago

#82 - build(deps): bump joblib from 1.0.1 to 1.2.0

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#81 - feature: doublet finding using knn with synthetic doublets

Pull Request - State: open - Opened by amcpherson almost 2 years ago

#80 - Readthedocs

Pull Request - State: closed - Opened by diljotgrewal almost 2 years ago

#79 - build(deps): bump nbconvert from 6.0.7 to 6.5.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#78 - build(deps): bump nbconvert from 6.0.7 to 6.3.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#77 - build(deps): bump mistune from 0.8.4 to 2.0.3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#76 - pip

Pull Request - State: closed - Opened by diljotgrewal almost 2 years ago

#75 - build(deps): bump numpy from 1.21.4 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#74 - build(deps): bump notebook from 6.2.0 to 6.4.12

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#73 - copy mm10.fa.fai into build

Pull Request - State: closed - Opened by soymintc about 2 years ago

#72 - build(deps): bump pyjwt from 1.7.1 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#71 - build(deps): bump notebook from 6.2.0 to 6.4.10

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#70 - build(deps): bump paramiko from 2.6.0 to 2.10.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#69 - build(deps): bump pillow from 8.1.2 to 9.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#68 - fix sorting error

Pull Request - State: open - Opened by adamcweiner over 2 years ago

#67 - edit requirements.txt

Pull Request - State: open - Opened by adamcweiner over 2 years ago

#66 - build(deps): bump django from 1.11.16 to 2.2.26

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#65 - build(deps): bump ipython from 7.9.0 to 7.16.3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#64 - Slight changes to cnplot functions

Pull Request - State: closed - Opened by adamcweiner over 2 years ago

#63 - build(deps): bump pillow from 8.1.2 to 9.0.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#62 - Anndataexperimental

Pull Request - State: closed - Opened by amcpherson over 2 years ago - 1 comment

#61 - mondrian loading, first pass

Pull Request - State: closed - Opened by amcpherson over 2 years ago - 1 comment

#60 - build(deps): bump django from 1.11.16 to 2.2.24

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#59 - build(deps): bump pillow from 8.1.2 to 8.3.2

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#58 - build(deps): bump notebook from 6.2.0 to 6.4.1

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#57 - Refactornotebooks

Pull Request - State: open - Opened by amcpherson almost 3 years ago

#56 - Loadingfixes

Pull Request - State: closed - Opened by amcpherson almost 3 years ago

#55 - refactor: snv loading updates and cleanup

Pull Request - State: closed - Opened by amcpherson almost 3 years ago

#54 - bugfix: change column name

Pull Request - State: open - Opened by marcjwilliams1 almost 3 years ago

#53 - error in load breakpoints

Issue - State: closed - Opened by marcjwilliams1 almost 3 years ago

#52 - build(deps): bump pillow from 8.1.2 to 8.2.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#51 - build(deps): bump urllib3 from 1.25.7 to 1.26.5

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#50 - minor: bugfix

Pull Request - State: closed - Opened by DouglasAbrams about 3 years ago

#49 - bugfix: mappability filtering

Pull Request - State: closed - Opened by amcpherson about 3 years ago

#48 - build(deps): bump urllib3 from 1.25.7 to 1.25.8

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#47 - changes for pseudobulk qc

Pull Request - State: open - Opened by DouglasAbrams about 3 years ago

#46 - feature: squashy cn profile

Pull Request - State: closed - Opened by amcpherson over 3 years ago

#45 - build(deps): bump pygments from 2.4.2 to 2.7.4

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#44 - build(deps): bump pyyaml from 5.1.2 to 5.4

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#43 - build(deps): bump jinja2 from 2.10.3 to 2.11.3

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#42 - build(deps): bump cryptography from 2.8 to 3.3.2

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#41 - build(deps): bump bleach from 3.0.2 to 3.3.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#40 - build(deps): bump notebook from 5.7.0 to 6.1.5

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#39 - build(deps): bump cryptography from 2.3.1 to 3.2

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#38 - special case lumpy assert fixed

Pull Request - State: closed - Opened by DouglasAbrams over 3 years ago

#37 - Retrieving pseudobulk data

Issue - State: open - Opened by nhuhoa almost 4 years ago

#36 - Run program in terminal mode - SNV analysis

Issue - State: open - Opened by nhuhoa almost 4 years ago

#35 - Issue with scgenome.snvphylo.snv_hierarchical_clustering_figure

Issue - State: open - Opened by nhuhoa almost 4 years ago - 1 comment

#34 - Deprecated function in snv_hierarchical_clustering_figure

Issue - State: open - Opened by nhuhoa almost 4 years ago

#33 - lumpy rearrangement types

Pull Request - State: closed - Opened by DouglasAbrams almost 4 years ago

#32 - refactor to allow for loading from files (#31)

Pull Request - State: closed - Opened by diljotgrewal almost 4 years ago - 1 comment

#31 - refactor to allow for loading from files

Pull Request - State: closed - Opened by DouglasAbrams almost 4 years ago

#30 - Fixcellcycle

Pull Request - State: closed - Opened by amcpherson almost 4 years ago

#29 - build(deps): bump django from 1.11.16 to 1.11.29

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#28 - build(deps): bump bleach from 3.0.2 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#27 - build(deps): bump bleach from 3.0.2 to 3.1.2

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#26 - bugfix: change assert to if statement

Pull Request - State: closed - Opened by marcjwilliams1 over 4 years ago

#25 - build(deps): bump psutil from 5.6.4 to 5.6.6

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#24 - build(deps): bump bleach from 3.0.2 to 3.1.1

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#23 - build(deps): bump django from 1.11.16 to 1.11.28

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#22 - refactor: loading new pseudobulk results

Pull Request - State: open - Opened by amcpherson over 4 years ago

#21 - Newloading

Pull Request - State: closed - Opened by amcpherson over 4 years ago

#20 - Update README.md

Pull Request - State: closed - Opened by Spenca over 4 years ago

#19 - bugfix: always prioritize a coding change if there is one

Pull Request - State: closed - Opened by amcpherson over 4 years ago

#18 - read_csv: load columns as str

Pull Request - State: closed - Opened by Spenca over 4 years ago

#17 - Readme updates

Pull Request - State: closed - Opened by Spenca over 4 years ago

#16 - edits to get_highest_snpeff_effect

Pull Request - State: closed - Opened by marcjwilliams1 over 4 years ago - 4 comments

#15 - slow load_snv_data

Issue - State: closed - Opened by marcjwilliams1 over 4 years ago - 3 comments

#14 - Test load pseudobulk fix

Pull Request - State: closed - Opened by Spenca over 4 years ago

#13 - Update .gitignore, requirements.txt

Pull Request - State: closed - Opened by Spenca over 4 years ago

#12 - build(deps): bump django from 1.11.16 to 1.11.23

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#11 - build(deps): bump urllib3 from 1.24.1 to 1.24.2

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#10 - build(deps): bump notebook from 5.7.0 to 5.7.8

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#9 - build(deps): bump pyyaml from 3.13 to 5.1

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#8 - Add _get_analysis_lanes functionality

Pull Request - State: closed - Opened by Spenca over 4 years ago

#7 - minor: added yaml files to package data

Pull Request - State: closed - Opened by diljotgrewal over 4 years ago

#6 - Inferclonesfix1

Pull Request - State: closed - Opened by amcpherson almost 5 years ago

#5 - Pseudobulkload

Pull Request - State: closed - Opened by amcpherson almost 5 years ago

#4 - refactor: analysis specific loaders, separate db from loading

Pull Request - State: closed - Opened by amcpherson almost 5 years ago

#3 - Scdna 115

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#2 - Newdata

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#1 - Add plot to README

Issue - State: closed - Opened by funnell almost 6 years ago - 3 comments

GitHub / shahcompbio/scgenome issues and pull requests