Ecosyste.ms: Issues

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GitHub / theislab/anndata2ri issues and pull requests

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#96 - Support DelayedMatrix assays

Issue - State: open - Opened by multimeric about 2 years ago
Labels: enhancement

#95 - Fix DataFrames in obsm

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

#94 - When I used the anndata2ri and rpy2, the error happened.

Issue - State: closed - Opened by melancholy12 about 2 years ago - 1 comment
Labels: invalid

#93 - scvelo cannot read the loom files

Issue - State: closed - Opened by mayurdoke6 about 2 years ago - 1 comment

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

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

#91 - Replace deprecated `rpy2.robjects.conversion.converter`

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

#90 - Exactly how to use LocalConverter to convert from AnnData to SCE within a normal Python script

Issue - State: closed - Opened by EdwardAgboraw about 2 years ago - 2 comments
Labels: question

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

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

#87 - cannot install anndata2ri

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

#86 - bioconda version out of date

Issue - State: closed - Opened by scottgigante-immunai over 2 years ago - 4 comments

#84 - R_HOME is None (MacOS Monterey 12.4)

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#82 - Better matrix conversion errors

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

#81 - Fix docs

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

#80 - Upgrade rpy2 to >= 3.4.3

Pull Request - State: closed - Opened by scottgigante-immunai over 2 years ago - 2 comments

#79 - Simplify docs

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

#78 - Fix compatibility with rpy2>=3.4.3

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

#77 - Fix compatibility with rpy2>=3.4.3

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

#76 - Fix docs

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

#75 - Fix deploy and bust correct cache

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

#74 - Fix publishing

Issue - State: closed - Opened by flying-sheep over 2 years ago

#73 - Reorganize and add pre-commit

Pull Request - State: closed - Opened by flying-sheep over 2 years ago - 2 comments

#72 - Move CI to GitHub Actions

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

#71 - Fix conversion for rpy2>3.4.2

Pull Request - State: closed - Opened by scottgigante over 2 years ago - 4 comments

#70 - na error in anndata2ri py2py_single_cell_experiment

Issue - State: closed - Opened by Hrovatin over 2 years ago - 2 comments

#69 - anndata2ri import breaks hdf5r import

Issue - State: closed - Opened by scottgigante-immunai over 2 years ago - 2 comments

#68 - int32 columns in obs break writing of adata to disk

Issue - State: open - Opened by le-ander almost 3 years ago - 1 comment

#67 - FileNotFoundError: [WinError 2] The system cannot find the file specified

Issue - State: closed - Opened by hyjforesight almost 3 years ago - 1 comment

#66 - Solve the incompatibility between scipy2ri and rpy2(version 3.4.3)

Pull Request - State: closed - Opened by liuzj039 about 3 years ago - 3 comments

#65 - Error converting Seurat object to SingleCellExperiment to anndata

Issue - State: closed - Opened by chris-rands over 3 years ago - 1 comment

#64 - cannot import name 'add_metaclass' from 'numba.core.utils'

Issue - State: closed - Opened by satellite119 over 3 years ago

#63 - Conversion broken with rpy2 3.4.3

Issue - State: closed - Opened by dburkhardt over 3 years ago - 24 comments

#62 - __call__() keywords must be strings

Issue - State: open - Opened by danli349 over 3 years ago - 1 comment

#61 - localconverter error

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

#60 - Use new scRNAseq package and fix rpy2 3.4 compat

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

#59 - output of `rpy2py_single_cell_experiment` may still be rpy2 objects

Issue - State: closed - Opened by scottgigante almost 4 years ago - 4 comments

#58 - TypeError when following sc-tutorial

Issue - State: open - Opened by mshirazi about 4 years ago - 4 comments

#56 - Fix docs

Pull Request - State: closed - Opened by flying-sheep about 4 years ago

#55 - unintuitive mapping for `adata.var`

Issue - State: closed - Opened by scottgigante about 4 years ago - 3 comments

#54 - Conversion to AnnData fails - R object with classes: ('SingleCellExperiment',) mapped to:

Issue - State: closed - Opened by MoritzTh about 4 years ago - 3 comments
Labels: invalid

#53 - Make Matrix conversion more resilient

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

#52 - Sort indices prior to conversion of csr/csc matrix

Pull Request - State: closed - Opened by scottgigante over 4 years ago - 3 comments

#50 - Conversion 'py2rpy' not defined for objects of type '<class 'numpy.ndarray'>'

Issue - State: closed - Opened by satellite119 over 4 years ago - 25 comments
Labels: bug

#49 - Allow any mapping to be converted

Pull Request - State: closed - Opened by ivirshup over 4 years ago - 1 comment

#48 - singleR error (Exception: Data must be 1-dimensional)

Issue - State: closed - Opened by jipeifeng over 4 years ago - 2 comments
Labels: needs info

#45 - RStudio crash when importing anndata2ri

Issue - State: closed - Opened by JLiLab over 4 years ago - 5 comments
Labels: duplicate

#44 - import error

Issue - State: closed - Opened by iosonofabio over 4 years ago - 7 comments
Labels: rpy2 / R

#43 - fail conversion with anndata 0.7.1

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

#42 - Conversion to R fails when adata.var is not empty

Issue - State: closed - Opened by climouse over 4 years ago - 2 comments
Labels: needs info

#41 - Convert factors to pd.Categorical

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

#40 - Problems with Seurat

Issue - State: closed - Opened by sergiopolid almost 5 years ago - 2 comments
Labels: invalid

#39 - Support converting factors in obs/var to pd.Series with CategoricalDtype

Issue - State: closed - Opened by apblair almost 5 years ago - 4 comments
Labels: bug

#38 - Exception with huge sparse matrices

Issue - State: closed - Opened by gokceneraslan almost 5 years ago - 1 comment
Labels: rpy2 / R

#37 - WIP fix Travis

Pull Request - State: closed - Opened by flying-sheep about 5 years ago

#36 - Fix anndata2ri.create_converter() example.

Pull Request - State: closed - Opened by gokceneraslan about 5 years ago - 1 comment

#35 - anndata2ri.activate() converts R vectors to numpy and makes names inaccessible

Issue - State: closed - Opened by gokceneraslan about 5 years ago - 1 comment
Labels: question

#34 - RuntimeError: found a situation in which we try to build a type recursively

Issue - State: closed - Opened by Yujing-Bio about 5 years ago - 1 comment
Labels: rpy2 / R

#33 - Fail to install on Windows

Issue - State: closed - Opened by fkoegel about 5 years ago - 2 comments
Labels: rpy2 / R

#32 - Conversion 'py2rpy' not defined for objects of type '<class 'anndata.core.anndata.AnnData'>'

Issue - State: closed - Opened by jphe about 5 years ago - 5 comments
Labels: invalid

#31 - AttributeError: 'Converter' object has no attribute 'py2rpy'

Issue - State: closed - Opened by sergiopolid about 5 years ago - 1 comment
Labels: invalid

#30 - add to bioconda

Issue - State: closed - Opened by grst about 5 years ago - 5 comments
Labels: enhancement

#29 - Seurat package won't load for anndata2ri conversion?

Issue - State: closed - Opened by Seandelao about 5 years ago - 3 comments
Labels: rpy2 / R

#28 - Cannot install anndata2ri

Issue - State: closed - Opened by grimwoo about 5 years ago - 2 comments
Labels: question

#26 - Udate: `np.matrix` conversion (issue #24)

Issue - State: closed - Opened by mumichae over 5 years ago - 1 comment
Labels: rpy2 / R

#25 - Error in installing anndata2ri

Issue - State: closed - Opened by aditisk over 5 years ago - 3 comments
Labels: invalid

#24 - Dense matrix conversion wrong

Issue - State: closed - Opened by mumichae over 5 years ago - 4 comments
Labels: rpy2 / R

#23 - Anndata2ri install fail

Issue - State: closed - Opened by ghost over 5 years ago - 3 comments
Labels: rpy2 / R

#22 - SyntaxError: future_fstrings

Issue - State: closed - Opened by aopisco over 5 years ago - 2 comments
Labels: invalid

#21 - Cannot install in Windows

Issue - State: closed - Opened by Ijoanito over 5 years ago - 4 comments
Labels: rpy2 / R

#20 - Use from R/reticulate host?

Issue - State: closed - Opened by flying-sheep over 5 years ago - 2 comments
Labels: enhancement

#18 - Error: "invalid class `dgRMatrix` object"

Issue - State: closed - Opened by LuckyMD over 5 years ago - 31 comments
Labels: scanpy / anndata

#17 - Support BiocSingular’s LowRankMatrix

Issue - State: open - Opened by LuckyMD over 5 years ago - 6 comments
Labels: enhancement

#16 - Dependencies?

Issue - State: closed - Opened by crichgriffin over 5 years ago - 2 comments
Labels: question

#15 - not following the conversion step

Issue - State: closed - Opened by MichaelPeibo over 5 years ago - 4 comments
Labels: question

#14 - unknown encoding:future_fstrings

Issue - State: closed - Opened by JuHey over 5 years ago - 2 comments
Labels: invalid

#12 - AnnData object without obsm produces error

Issue - State: closed - Opened by fidelram over 5 years ago - 2 comments
Labels: bug

#11 - 'Converter' object has no attribute 'py2rpy'

Issue - State: closed - Opened by fidelram over 5 years ago - 3 comments
Labels: rpy2 / R

#10 - Converting adata object with neighbour graph produces error

Issue - State: closed - Opened by le-ander over 5 years ago - 2 comments
Labels: bug

#9 - Map reducedDims↔.obsm names

Issue - State: closed - Opened by flying-sheep over 5 years ago
Labels: enhancement

#8 - Implement support for sparse matrices

Issue - State: closed - Opened by flying-sheep over 5 years ago - 6 comments
Labels: enhancement

#6 - implement obsm→reducedDims

Issue - State: closed - Opened by flying-sheep over 5 years ago
Labels: enhancement

#4 - Support reducedDims↔.obsm

Issue - State: closed - Opened by flying-sheep over 5 years ago
Labels: enhancement

#3 - Support .var_names/.obs_names→rownames/colnames

Issue - State: closed - Opened by flying-sheep almost 6 years ago
Labels: enhancement

#2 - Make travis work

Issue - State: closed - Opened by flying-sheep almost 6 years ago - 2 comments
Labels: enhancement

#1 - Support metadata→.obs

Issue - State: closed - Opened by flying-sheep almost 6 years ago
Labels: enhancement