Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / parashardhapola/scarf issues and pull requests

#139 - Zarr > 2.16.0 breaks Scarf on S3

Issue - State: open - Opened by oskbor about 1 month ago

#138 - Use less aggressive filtering for small datasets

Pull Request - State: closed - Opened by oskbor 2 months ago - 1 comment

#137 - DatasetMerge fix

Pull Request - State: closed - Opened by Gautam8387 2 months ago

#136 - Fixed `dask` version for better performance

Pull Request - State: closed - Opened by Gautam8387 2 months ago

#135 - Fix for `get_feat_suffix()`

Pull Request - State: closed - Opened by Gautam8387 3 months ago

#134 - Updated consume() in CrDirReader [Polars -> Pandas]

Pull Request - State: closed - Opened by Gautam8387 4 months ago

#133 - Update Mark HVGS

Pull Request - State: closed - Opened by Gautam8387 4 months ago

#132 - ZarrMerge writer import for backwards compatibility.

Pull Request - State: closed - Opened by Gautam8387 4 months ago

#131 - Addition of Metric Calculation Methods

Pull Request - State: closed - Opened by Gautam8387 4 months ago

#130 - CrDirReader Update [Polars -> Pandas]

Pull Request - State: closed - Opened by Gautam8387 4 months ago

#129 - Fix mapping key

Pull Request - State: closed - Opened by oskbor 4 months ago

#128 - Fall back to using feature names when mapping

Pull Request - State: closed - Opened by oskbor 4 months ago

#126 - Support for BD formatted mtx files

Issue - State: open - Opened by oskbor 5 months ago

#125 - Added Support For Merging Multiple DataStore and Handling Different Assay Types

Pull Request - State: closed - Opened by Gautam8387 6 months ago - 2 comments

#124 - Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#122 - Use target cell_key when mapping

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

#121 - Support raw (unfiltered) matrices in CrDirReader

Issue - State: closed - Opened by oskbor 6 months ago - 1 comment

#120 - Scarf core package

Issue - State: open - Opened by oskbor 6 months ago

#119 - Merging datasets with different amount of features. Is it possible?

Issue - State: closed - Opened by olferievm 7 months ago - 1 comment

#118 - pip install scarf issue

Issue - State: closed - Opened by olferievm 8 months ago

#117 - error at step: ds.plot_marker_heatmap

Issue - State: open - Opened by JelenaKrneta 8 months ago

#115 - Fixes for parallell runs

Pull Request - State: closed - Opened by oskbor 9 months ago - 1 comment

#114 - Conversion from anndata to zarr and umap visualization

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

#113 - Doublet detection

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

#112 - Error in conversion from AnnData to Zarr

Issue - State: open - Opened by stefraptis about 1 year ago

#110 - Production release with a version bump

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

#109 - Production release

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

#107 - Allow mapping using gene names

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

#106 - Interoperability documentation - Scanpy

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

#105 - Use thread pool executor

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

#104 - using ThreadPoolExecutor instead of ThreadPool to avoid semlock

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

#103 - Typos and small documentation improvements

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

#102 - ZarrMerge behaves weirdly

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

#101 - Production release

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

#100 - Production release

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

#99 - Production release

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

#98 - Production release

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

#97 - Fixes/pseudotime

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

#96 - bug, typing and docstring fixes

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

#95 - Production release

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

#94 - Improvements in make_bulk

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

#93 - added support for reading unfiltered cellranger h5 files

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

#92 - Added HTO demultiplexing feature

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

#91 - Feature/harmony

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

#89 - Unsure what this error message is trying to tell me

Issue - State: open - Opened by aichander almost 2 years ago

#88 - version bump

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

#87 - bug fix in SubsetZarr when using workspace

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

#86 - Exposed ann_index helpers in run_mapping

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

#85 - fixed workspace related bug in mapping_utils

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

#83 - Update README.rst

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

#82 - How to add feature name changed by gene name?

Issue - State: closed - Opened by melancholy12 over 2 years ago - 2 comments
Labels: how-to

#81 - cannot make UMAP

Issue - State: closed - Opened by melancholy12 over 2 years ago - 4 comments
Labels: upstream

#77 - Error: Conversion Anndata to Scarf’s Zarr format file

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

#74 - Documentation enhancement for SubsetZarr

Issue - State: closed - Opened by stela2502 over 2 years ago - 1 comment

#73 - Support for Trimodal multiomic data analysis

Issue - State: open - Opened by bioarpit1 over 2 years ago

#72 - ds.to_anndata() and scarf.writers.to_h5ad() crteate two different data structures

Issue - State: closed - Opened by stela2502 over 2 years ago - 4 comments
Labels: bug, enhancement

#71 - ZarrMerge producing empty counts while .zarr files used to merge have associated counts?

Issue - State: closed - Opened by marhirst over 2 years ago - 6 comments
Labels: how-to

#70 - h5py - minimal requirement

Issue - State: closed - Opened by stela2502 over 2 years ago
Labels: upstream

#67 - run_clustering() error using Paris clustering algorithm

Issue - State: closed - Opened by sandhusumiti over 2 years ago - 2 comments
Labels: bug, cant-reproduce

#66 - starting to submit some tests

Pull Request - State: closed - Opened by razofz almost 3 years ago - 2 comments

#65 - clusters input for TopACeDo

Issue - State: closed - Opened by yuhanH about 3 years ago - 3 comments
Labels: question

#64 - ATAC-seq recognized as RNA-seq?

Issue - State: closed - Opened by arita-clavy about 3 years ago - 2 comments

#63 - How do you reset the column "I" ?

Issue - State: closed - Opened by m0nib over 3 years ago - 9 comments
Labels: question

#62 - If the assay is not RNA - e.g. spliced from a kallisto/bustools run

Issue - State: closed - Opened by stela2502 over 3 years ago - 2 comments
Labels: question

#61 - loom file from kallisto/bustools import error:

Issue - State: closed - Opened by stela2502 over 3 years ago - 9 comments
Labels: bug, upstream

#60 - a problem import scarf (wrong version of tqdm)

Issue - State: closed - Opened by liuweihanty over 3 years ago - 3 comments
Labels: question, upstream

#59 - can I convert and import Seurat/SCE object to scarf

Issue - State: closed - Opened by liuweihanty over 3 years ago - 3 comments
Labels: documentation, good first issue, question

#58 - Normalization of ADTs on merged datasets

Issue - State: closed - Opened by rwarfvinge over 3 years ago - 6 comments
Labels: more info needed

#57 - Additonal feature request to ds.plot_layout()

Issue - State: open - Opened by rwarfvinge over 3 years ago - 3 comments
Labels: enhancement

#54 - Constructing a scarf Zarr dataset from scratch

Issue - State: closed - Opened by jamestwebber over 3 years ago - 1 comment
Labels: documentation, question

#53 - Added CodeCov GH action

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

#52 - Update issue templates

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

#51 - Development

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

#50 - Package name on PyPi

Issue - State: closed - Opened by parashardhapola over 3 years ago - 1 comment
Labels: wontfix

#49 - High memory consumption by Dask arrays

Issue - State: closed - Opened by parashardhapola over 3 years ago - 5 comments
Labels: upstream

#48 - test datastore class

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

#47 - Plotting vignette + minor fix to colorbar padding in grid plots

Pull Request - State: closed - Opened by JohanRodhe over 3 years ago - 1 comment

#41 - fixed wget bug

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

#40 - fix .circleci/config.yml

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

#39 - Development

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

#38 - Grid plotting

Pull Request - State: closed - Opened by JohanRodhe over 3 years ago - 1 comment

#37 - export cluster markers

Issue - State: closed - Opened by sommarin over 3 years ago - 1 comment
Labels: more info needed

#36 - Grid plotting

Pull Request - State: closed - Opened by JohanRodhe over 3 years ago - 1 comment

#35 - vignette step fails due to missing SG-tSNE libs

Issue - State: closed - Opened by razofz over 3 years ago - 2 comments
Labels: documentation, wontfix

#34 - API documentation on readthedocs

Issue - State: closed - Opened by razofz over 3 years ago - 1 comment
Labels: documentation, question

#33 - Docstrings, task list

Issue - State: closed - Opened by razofz over 3 years ago - 1 comment
Labels: documentation

#32 - retain QC filtering and columns after scarf.make.subset()

Issue - State: closed - Opened by rwarfvinge over 3 years ago - 2 comments

#31 - docstrings, mostly {readers,writers}.py

Pull Request - State: closed - Opened by razofz over 3 years ago - 8 comments

#30 - Rename ds.cells.columns?

Issue - State: closed - Opened by rwarfvinge over 3 years ago - 2 comments
Labels: enhancement, question, wontfix

#29 - Missing figure legends in PNGs

Issue - State: closed - Opened by rwarfvinge over 3 years ago - 3 comments
Labels: bug

#28 - Retain QC filtering after scarf.ZarrMerge()?

Issue - State: closed - Opened by rwarfvinge over 3 years ago - 2 comments
Labels: enhancement

#27 - adjusting filtering parameters in ds.filter_cells()

Issue - State: closed - Opened by rwarfvinge over 3 years ago - 2 comments
Labels: bug, enhancement

#26 - added env info in install + minor changes in vignettes

Pull Request - State: closed - Opened by JohanRodhe over 3 years ago - 1 comment

#25 - working towards fuller docstring coverage (atm 50%)

Pull Request - State: closed - Opened by razofz almost 4 years ago - 2 comments

#24 - Drop column not dropping

Issue - State: closed - Opened by sommarin almost 4 years ago - 1 comment
Labels: bug

#23 - Computing kNN graphs on user-provided dimensional reductions?

Issue - State: closed - Opened by davisidarta almost 4 years ago - 8 comments
Labels: good first issue