scverse/anndataR

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AnnData interoperability in R

Stars: 196
Forks: 22
Open beginner issues: 0
Indexed issues: 40
Avg merge: 1d 9h
Merged PRs (30d): 7

Dominant language: R
License: No license data
Last GitHub push: Sep 17, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

40 open issues indexed

Test reading/writing H5AD files across multiple anndata releases Open

developer h5ad

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/anndataR#516 · 1 reaction · Opened Aug 31, 2026
Add anndataR to scverse/integration-testing Open

developer

Difficulty 4/5 3-5 days Newbie friendliness 48/100

scverse/anndataR#515 · 1 reaction · Opened Aug 31, 2026
Full support for Python anndata >= 0.13 Open

new feature

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/anndataR#514 · 3 comments · Opened Aug 31, 2026
Implement compression for boolean datasets Open

h5ad new feature

Difficulty 3/5 1-2 days Newbie friendliness 76/100

scverse/anndataR#513 · Opened Aug 31, 2026
usage_python vignette fails with mudata >= 0.4 Open

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

scverse/anndataR#511 · Opened Aug 31, 2026
Spec deviation for Zarr scalar strings Open

bug triage

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/anndataR#500 · 2 comments · Opened Aug 12, 2026
Seurat object CITE-seq data conversion do AnnData, scanpy read issue Open

question triage

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/anndataR#494 · 3 comments · Opened Jul 29, 2026
hdf5_adata$as_Seurat fails when features contain `_` Open

bug triage

Difficulty 3/5 1-2 days Newbie friendliness 55/100

scverse/anndataR#476 · 3 comments · Opened Jul 9, 2026
Add lazy hdf5anndata to benchmarks Open

triage

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

scverse/anndataR#474 · Opened Jun 23, 2026
Allow reading/writing from a path in a HDF5 file Open

h5ad triage

scverse/anndataR#466 · 1 reaction · 1 assignee · Opened Jun 11, 2026
Consolidated Zarr metadata at the root of the anndata zarr store Open

triage

Difficulty 3/5 1-2 days Newbie friendliness 50/100

scverse/anndataR#461 · 1 comment · Opened May 25, 2026
Add optional data.frame conversion for Matrix column names (Seurat Conversion) Open

triage

Difficulty 3/5 1-2 days Newbie friendliness 58/100

scverse/anndataR#459 · Opened May 21, 2026
Extract shared encoding helpers from H5AD and Zarr backends Open

h5ad zarr

Difficulty 4/5 3-5 days Newbie friendliness 68/100

scverse/anndataR#445 · Opened Apr 15, 2026
Investigate how missing values are handled in string arrays Open

h5ad zarr

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/anndataR#444 · 1 reaction · Opened Apr 15, 2026
Does `.view$as_HDF5AnnData(file = subset_file_path)` copy all data to the memory before writing to the disk? Open

h5ad question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/anndataR#433 · Opened Mar 6, 2026
Add support for scATAC-seq data Open

new feature

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/anndataR#414 · 1 comment · Opened Feb 6, 2026
Improve `rec-array` conformance between anndataR and anndata(py) Open

design

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/anndataR#409 · 8 comments · Opened Jan 22, 2026
Awkward array support Open

h5ad

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/anndataR#404 · 2 comments · Opened Dec 31, 2025
`UnicodeDecodeError` when reading H5AD in Python Open

h5ad needs info

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/anndataR#400 · 1 comment · Opened Dec 12, 2025
Add support for Seurat v4 objects Open

new feature Seurat

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/anndataR#399 · 3 comments · Opened Dec 9, 2025
Error: `rownames(X)` is not as expected Open

SingleCellExperiment

Difficulty 3/5 1-2 days Newbie friendliness 38/100

scverse/anndataR#390 · 4 comments · Opened Dec 2, 2025
Assay in `SingleCellExperiment` not being transposed Open

SingleCellExperiment

scverse/anndataR#388 · 9 comments · 1 assignee · Opened Dec 1, 2025
Store an `output_class` vector somehere? Open

developer ux

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

scverse/anndataR#385 · 1 comment · Opened Nov 24, 2025
Move conversion functions to `{zellkonverter}`? Open

design question

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/anndataR#383 · Opened Nov 20, 2025
Explore alternative matrix classes Open

design performance

scverse/anndataR#382 · 1 reaction · 1 assignee · Opened Nov 20, 2025
Add lazy named list to reduce memory usage Open

performance

scverse/anndataR#353 · 5 comments · 1 assignee · Opened Sep 23, 2025
Add `$copy()` to AbstractAnnData Open

design new feature question

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/anndataR#352 · 1 comment · Opened Sep 22, 2025
Error when converting spatial data Open

needs info Seurat

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/anndataR#338 · 1 comment · Opened Sep 22, 2025
Support for spatial transcriptomics (Visium) Open

new feature

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/anndataR#337 · 1 comment · Opened Sep 19, 2025
Add a `mapping_spec` class/function Open

new feature question

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/anndataR#336 · Opened Sep 17, 2025
Unusually high memory usage for `{anndataR}` compared to Python `anndata` Open

performance

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/anndataR#329 · 11 comments · 1 reaction · Opened Aug 30, 2025
Add `concat` functionality Open

new feature

scverse/anndataR#325 · 1 comment · 1 assignee · Opened Aug 25, 2025
Error `NAs introduced by coercion to integer range` when reading large H5AD Open

performance

Difficulty 4/5 3-5 days Newbie friendliness 42/100

scverse/anndataR#301 · 5 comments · Opened Jul 23, 2025
Should `generate_matrix()` handle `logical` and `character` types? Open

generation question

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/anndataR#288 · 1 comment · Opened Jun 27, 2025
Handle conversion of SCT output Open

Seurat

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/anndataR#271 · 1 comment · 1 reaction · Opened May 20, 2025
Add a `raw` slot Open

design

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/anndataR#259 · 3 comments · 2 reactions · Opened Apr 9, 2025
Store `var_names`/`obs_names` as fixed-size types? Open

design question

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/anndataR#172 · 1 comment · Opened Jul 8, 2024
Support reading H5AD files from `anndata` < 0.8.0? Open

question

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/anndataR#134 · 4 comments · Opened Oct 13, 2023
Store `obs_names` and `var_names` as character? Open

design question

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/anndataR#73 · 4 comments · Opened May 6, 2023
Coordinating with `scKirby` Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

scverse/anndataR#71 · 3 comments · Opened May 5, 2023

scverse/anndataR

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