Ecosyste.ms: Issues

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

GitHub / scverse/muon issues and pull requests

#146 - filter_obs is broken with latest AnnData

Issue - State: open - Opened by grst 3 months ago
Labels: bug

#145 - CUPY memory allocation error when running MOFA

Issue - State: open - Opened by wlason 3 months ago
Labels: bug

#143 - :bug: fix counts_fragments_features

Pull Request - State: open - Opened by mbuttner 6 months ago - 1 comment

#142 - WNN integration raise error while adding connectivities into mdata.obsp

Issue - State: open - Opened by 5tinzi 6 months ago
Labels: bug

#141 - Error with muon import

Issue - State: closed - Opened by Connorr0 6 months ago - 3 comments
Labels: bug

#139 - Invalid function call in independent component analysis (tl.ica)

Issue - State: open - Opened by pavanvidem 7 months ago
Labels: bug

#138 - Test against pre-releases

Issue - State: open - Opened by ivirshup 7 months ago
Labels: enhancement

#137 - Improve module import time

Issue - State: open - Opened by rpadmanabhan 8 months ago - 1 comment
Labels: enhancement

#136 - scanpy 1.10 compat + PR CI

Pull Request - State: closed - Opened by ivirshup 8 months ago - 4 comments

#135 - ImportError: cannot import name '_compute_connectivities_umap' from 'scanpy.neighbors'

Issue - State: closed - Opened by nbutyrate 8 months ago - 9 comments
Labels: bug

#134 - Fix #132

Pull Request - State: open - Opened by SarahOuologuem 8 months ago - 1 comment

#133 - Add fragment file path to a merged mudata object

Issue - State: open - Opened by jolvhull 9 months ago - 1 comment
Labels: enhancement

#132 - mu.pl.scatter() fails when providing color

Issue - State: open - Opened by SarahOuologuem 9 months ago
Labels: bug

#130 - float overflow in dsb normalization

Issue - State: open - Opened by javiermarchena 9 months ago - 1 comment
Labels: bug

#128 - ValueError: could not broadcast input array from shape

Issue - State: open - Opened by wariobrega 12 months ago - 2 comments
Labels: bug

#127 - How can I concatenate multiple `muon` data samples?

Issue - State: closed - Opened by danli349 about 1 year ago - 2 comments

#126 - raw is also normalized with clr

Issue - State: closed - Opened by GirayEryilmaz about 1 year ago - 4 comments
Labels: bug

#125 - Sum duplicate rows in muon.atac.tl.count_fragments_features

Issue - State: open - Opened by benjamin-james about 1 year ago
Labels: enhancement

#124 - Enable `gene_symbols` argument in mu.pl.embedding

Issue - State: open - Opened by racng about 1 year ago - 1 comment
Labels: enhancement

#123 - Batch correction for joint modality umap

Issue - State: open - Opened by GirayEryilmaz about 1 year ago
Labels: enhancement

#122 - MOFA error when data has been created using `axis=-1`

Issue - State: open - Opened by dawe about 1 year ago
Labels: bug

#121 - Is being developed?

Issue - State: closed - Opened by GirayEryilmaz over 1 year ago - 2 comments
Labels: enhancement

#119 - "OptionError: 'Pattern matched multiple keys'" traceback in tutorial

Issue - State: open - Opened by chris-rands over 1 year ago
Labels: bug

#117 - Add NumFocus logo and text

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

#116 - Negative values after pt.pp.dsb

Issue - State: open - Opened by ChaseTaylor939 over 1 year ago - 1 comment
Labels: bug

#115 - Error when writing .obsm of MuData object

Issue - State: closed - Opened by CarstenKnutsen over 1 year ago - 1 comment
Labels: bug

#114 - :sparkles: Extend _l2norm for sparse input

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

#113 - MOFA on multiple groups with single view

Issue - State: open - Opened by martinrohbeck over 1 year ago - 1 comment
Labels: enhancement

#112 - Fixes scverse/muon#111

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

#111 - Numpy IndexError in muon._core.tools.mofa

Issue - State: closed - Opened by russellgould over 1 year ago - 2 comments
Labels: bug

#110 - Count fragment function counts duplicates

Issue - State: open - Opened by lauradmartens over 1 year ago
Labels: bug

#109 - Fix save color in MuData

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

#108 - ac.pl.umap error message "ValueError: no types given"

Issue - State: closed - Opened by ad7115 over 1 year ago - 2 comments
Labels: bug

#107 - Tutorials for integrating BCR or TCR analysis with muon

Issue - State: open - Opened by zenghk over 1 year ago
Labels: enhancement

#105 - ac.tl.nucleosome_signal bug

Issue - State: closed - Opened by ad7115 over 1 year ago - 3 comments
Labels: bug

#104 - Incompatibilities with latest numpy

Issue - State: closed - Opened by grst over 1 year ago
Labels: bug

#103 - Adopt cookiecutter-scverse template

Issue - State: open - Opened by grst over 1 year ago
Labels: enhancement

#101 - How should I save the `ac.pl.fragment_histogram()` plot?

Issue - State: closed - Opened by danli349 over 1 year ago - 1 comment
Labels: bug

#100 - Add scverse citation

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

#97 - Broken link: tutorial for cell type annotation

Issue - State: open - Opened by yangjun9095 over 1 year ago
Labels: bug

#96 - Can't mix variables from obs and var in `pl.embedding`

Issue - State: closed - Opened by grst over 1 year ago
Labels: bug

#95 - Confusing error message on missing key in `pl.embeddings`

Issue - State: closed - Opened by grst over 1 year ago - 1 comment
Labels: bug

#93 - Intersect obs fails if AnnData doesn't have X

Issue - State: closed - Opened by grst almost 2 years ago
Labels: bug

#91 - `sklearn` vs `scikit-learn`

Issue - State: closed - Opened by gjhuizing almost 2 years ago - 4 comments
Labels: bug

#90 - Any plan to add footprints module for ATAC-seq?

Issue - State: open - Opened by lzj1769 almost 2 years ago - 1 comment
Labels: enhancement

#89 - Bugs in muon.pp.neighbors(mdata, key_added='wnn')

Issue - State: closed - Opened by HelloWorldLTY almost 2 years ago - 6 comments

#88 - ValueError: could not convert integer scalar

Issue - State: closed - Opened by alexlenail almost 2 years ago - 3 comments
Labels: bug

#87 - Clearer documentation for `ac.tl.lsi`

Issue - State: open - Opened by alexlenail almost 2 years ago - 1 comment
Labels: enhancement

#86 - Segmentation fault in mu.neighbor

Issue - State: open - Opened by Feilijiang almost 2 years ago - 3 comments
Labels: bug

#83 - `python setup.py egg_info did not run successfully.` during install

Issue - State: closed - Opened by danli349 almost 2 years ago - 1 comment
Labels: bug

#82 - raise error when mu.pp.neighbors

Issue - State: closed - Opened by 111kakaluote almost 2 years ago - 2 comments
Labels: bug

#81 - core dumped when run 'mu.pp.neighbors(mdata, key_added='wnn')'

Issue - State: open - Opened by 111kakaluote almost 2 years ago - 4 comments

#78 - Add link to GitHub page on Muon docs

Issue - State: closed - Opened by gregjohnso almost 2 years ago - 1 comment
Labels: enhancement

#77 - Batch correction with MOFA

Issue - State: closed - Opened by alitinet about 2 years ago - 2 comments

#76 - When the input is Anndata, the mefisto model cannot be saved

Issue - State: closed - Opened by liuzj039 about 2 years ago
Labels: bug

#75 - GPU not found

Issue - State: closed - Opened by wangjiawen2013 about 2 years ago - 1 comment
Labels: bug

#74 - save data on disk error

Issue - State: closed - Opened by wangjiawen2013 about 2 years ago - 4 comments
Labels: bug

#73 - Illegal instruction: 4

Issue - State: closed - Opened by msenosain about 2 years ago - 2 comments
Labels: bug

#72 - Update pyproject.toml, Fix wrong sklearn dependency.

Pull Request - State: closed - Opened by moinfar about 2 years ago - 1 comment

#71 - missing index file atac fragments

Issue - State: closed - Opened by bio-la about 2 years ago - 2 comments
Labels: enhancement

#70 - Improve mofa interface

Issue - State: closed - Opened by gtca over 2 years ago - 1 comment
Labels: enhancement

#68 - muon.atac.tl.count_fragments_features atac bug

Issue - State: open - Opened by Chengwei94 over 2 years ago - 2 comments
Labels: bug

#67 - Use a representation from mudata.obsm to calculate neighbors

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

#66 - a small BUG in mu.tl.mofa

Issue - State: closed - Opened by liujilei156231 over 2 years ago - 1 comment
Labels: bug

#65 - Can't save MuData object to h5mu file due to OrderedDict

Issue - State: closed - Opened by PauBadiaM over 2 years ago - 3 comments
Labels: bug

#64 - concatenate muon objects

Issue - State: open - Opened by vjbaskar over 2 years ago - 1 comment
Labels: enhancement

#63 - ATACseq+RNAseq Integration Tutorial Error Loading Data

Issue - State: closed - Opened by the-rich-piana over 2 years ago - 6 comments
Labels: bug

#62 - High Cpu Usage

Issue - State: closed - Opened by liujilei156231 over 2 years ago - 3 comments

#61 - Shape Issue with mu.tl.mofa

Issue - State: closed - Opened by Chadmiumoxid over 2 years ago - 6 comments

#60 - Documentation for `muon.atac.tl.scan_sequences` not up to date

Issue - State: open - Opened by gjhuizing over 2 years ago - 1 comment
Labels: documentation, atac

#59 - Incorrect behavior in muon.atac.tl.count_fragments_features

Issue - State: open - Opened by kchiou over 2 years ago - 2 comments
Labels: bug, atac

#58 - View distal/promoter peaks after RNA/ATAC integration

Issue - State: closed - Opened by matthew-levy over 2 years ago - 2 comments
Labels: enhancement

#57 - Can't save MuData object to h5mu file

Issue - State: closed - Opened by josenachorr over 2 years ago - 15 comments
Labels: bug

#56 - pysam installation issue on Windows

Issue - State: closed - Opened by khanthanan over 2 years ago - 3 comments
Labels: bug

#55 - conda package

Issue - State: closed - Opened by Zethson over 2 years ago - 9 comments
Labels: enhancement

#54 - Peak GC content quantification in ATAC module

Issue - State: open - Opened by emdann over 2 years ago - 1 comment
Labels: enhancement, atac

#52 - Error in mu.tl.mofa

Issue - State: closed - Opened by Chengwei94 over 2 years ago - 2 comments
Labels: bug

#51 - error in function ac.pl.fragment_histogram(atac, region=''")

Issue - State: closed - Opened by Raselel over 2 years ago - 8 comments
Labels: bug, atac

#50 - Plotting function should document parameters better

Issue - State: open - Opened by gtca almost 3 years ago
Labels: enhancement, good first issue

#49 - Exporting or saving plots to pdf file

Issue - State: closed - Opened by francat almost 3 years ago - 4 comments
Labels: enhancement

#48 - CITE-seq scatter plot of pairwise RNA-prot correlations

Issue - State: closed - Opened by chris-rands almost 3 years ago - 3 comments
Labels: enhancement

#47 - Added options to run mofa in SVI mode

Pull Request - State: closed - Opened by sagar87 almost 3 years ago - 1 comment

#46 - Update tools.py

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

#45 - Datasets module

Issue - State: open - Opened by ivirshup almost 3 years ago - 3 comments
Labels: enhancement

#44 - mu.pp.intersect_obs introduces Nans to mdata.obs

Issue - State: closed - Opened by crichgriffin almost 3 years ago - 2 comments
Labels: bug

#43 - can't perform sequential mu.pp.filter_obs

Issue - State: closed - Opened by crichgriffin almost 3 years ago - 2 comments
Labels: bug

#42 - Update dsb interface

Issue - State: open - Opened by gtca about 3 years ago
Labels: enhancement, prot

#41 - Use mudata as a dependency

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