BiocPy/SummarizedExperiment issues and pull requests

#80 - Fix in-place when updating row or column data

Pull Request - State: closed - Opened by jkanche 25 days ago

#79 - `in_place` has no effect when `replace_column_names` is also set to True

Issue - State: closed - Opened by DiDeoxy 30 days ago - 3 comments

#78 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] about 2 months ago

#77 - Inconsistencies with R SummarizedExperiment and RangedSummarizedExperiment

Issue - State: open - Opened by DiDeoxy 3 months ago - 2 comments

#76 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#75 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#74 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#73 - Use admonitions

Pull Request - State: closed - Opened by jkanche 6 months ago

#72 - Sync docs with tutorial

Pull Request - State: closed - Opened by jkanche 6 months ago

#71 - Fix a bug when exporting objects as `AnnData`

Pull Request - State: closed - Opened by jkanche 7 months ago

#70 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#69 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#68 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#67 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#66 - warn when delayedarray's are fully realized into memory

Pull Request - State: closed - Opened by jkanche 10 months ago

#65 - Conversion to AnnData if matrices are delayedarrays or filebacked

Pull Request - State: closed - Opened by jkanche 10 months ago

#64 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#63 - Fix typo in `set_row_ranges`

Pull Request - State: closed - Opened by jkanche 10 months ago

#62 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#61 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#60 - Missing `row_ranges` in RSE `str`

Issue - State: open - Opened by jkanche 11 months ago
Labels: enhancement, good first issue

#59 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#58 - update CHANGELOG

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

#57 - warn when row_data or column_data's row_names are not unique.

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

#56 - Refactor logic between row_names from SE and row/column data

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

#55 - setters should be able to reset/remove attributes

Issue - State: closed - Opened by jkanche 11 months ago

#54 - test across different versions

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

#53 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago

#52 - Overhaul SE

Pull Request - State: closed - Opened by jkanche almost 1 year ago - 2 comments

#51 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#50 - Why is `se.metadata` capable of being `None`?

Issue - State: closed - Opened by LTLA about 1 year ago - 1 comment

#49 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#48 - Implement combine generic

Pull Request - State: closed - Opened by jkanche about 1 year ago - 1 comment

#47 - Eliminated the hard-ish AnnData dependency.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#46 - Eliminate scipy dependency

Issue - State: closed - Opened by LTLA about 1 year ago - 2 comments

#45 - Eliminate unnecessary dependency on filebackedarray.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#44 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#43 - slice row_ranges on rse

Pull Request - State: closed - Opened by jkanche about 1 year ago

#42 - bump granges, simplify typehints

Pull Request - State: closed - Opened by jkanche about 1 year ago

#41 - bump genomic ranges package

Pull Request - State: closed - Opened by jkanche about 1 year ago

#40 - access an assay by index

Pull Request - State: closed - Opened by jkanche about 1 year ago

#39 - issues with combine cols

Issue - State: closed - Opened by jkanche about 1 year ago - 1 comment

#38 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#37 - prefer biocframe over pandas

Issue - State: closed - Opened by jkanche about 1 year ago - 2 comments

#36 - support GRL in RSE

Pull Request - State: closed - Opened by jkanche about 1 year ago

#35 - Support GenomicRangesList

Issue - State: closed - Opened by DiDeoxy about 1 year ago - 1 comment

#34 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#33 - Show granges warn

Pull Request - State: closed - Opened by jkanche about 1 year ago

#32 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#31 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#30 - update pre-commit config

Pull Request - State: closed - Opened by jkanche over 1 year ago

#29 - update pre-commit config

Pull Request - State: closed - Opened by jkanche over 1 year ago

#28 - Pythonify

Pull Request - State: closed - Opened by jkanche over 1 year ago - 1 comment

#27 - propagate `firstMatch` parameter in `get_indexes_from_names()` upstream

Issue - State: closed - Opened by keviny2 over 1 year ago - 2 comments

#26 - split by annotation

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

#25 - warning when initializing SE: if rowdata is genomic ranges

Issue - State: closed - Opened by jkanche over 1 year ago

#24 - feat: allow slicing by name when there are duplicates

Pull Request - State: closed - Opened by keviny2 over 1 year ago

#23 - needs an axis or dimension parameter

Issue - State: closed - Opened by jkanche over 1 year ago

#22 - feat: slice by name when there are duplicates

Pull Request - State: closed - Opened by keviny2 over 1 year ago - 3 comments

#21 - subsetting when there are duplicate index names

Issue - State: closed - Opened by keviny2 over 1 year ago

#20 - strictly enforce indexes aka rownames/colnames?

Issue - State: closed - Opened by jkanche over 1 year ago

#19 - `rowData` and `colData` are empty if use bool or str array to slice

Issue - State: closed - Opened by keviny2 over 1 year ago - 1 comment

#18 - implement an iterator

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

#17 - if `pd.concat` is all we need

Pull Request - State: closed - Opened by jkanche over 1 year ago - 4 comments

#16 - feat: combineCols()

Pull Request - State: closed - Opened by keviny2 over 1 year ago - 5 comments

#15 - feat: combineCols()

Pull Request - State: closed - Opened by keviny2 over 1 year ago

#14 - chore: update email

Pull Request - State: closed - Opened by keviny2 over 1 year ago

#13 - Slice SE by names

Pull Request - State: closed - Opened by jkanche over 1 year ago

#12 - feat: slice by name

Pull Request - State: closed - Opened by keviny2 over 1 year ago - 1 comment

#11 - enable slicing by name

Issue - State: closed - Opened by keviny2 over 1 year ago - 1 comment

#10 - feat: a number of minor changes

Pull Request - State: closed - Opened by jkanche over 1 year ago

#9 - feat: implement combineCols()

Pull Request - State: closed - Opened by keviny2 over 1 year ago

#8 - support H5 backed assays in SE

Pull Request - State: closed - Opened by jkanche over 1 year ago

#7 - Dev/maxh

Pull Request - State: closed - Opened by DiDeoxy over 1 year ago - 3 comments

#6 - `rowData` and `colData` needs to set an empty biocframe object

Issue - State: closed - Opened by jkanche over 1 year ago - 1 comment

#5 - protobuf as a data exchange format

Issue - State: closed - Opened by jkanche almost 2 years ago

#4 - interface with mospy's `rowsums` and `colsums`

Issue - State: closed - Opened by jkanche almost 2 years ago

#3 - revamp SE, RSE classes

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

#2 - support `backed` mode with delayed access to the matrix

Issue - State: closed - Opened by jkanche over 2 years ago - 1 comment

#1 - feat: subset SE/RSE by indices

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

GitHub / BiocPy/SummarizedExperiment issues and pull requests