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Running sc.pp.highly_variable_genes(adata, n_top_genes=5000, flavor='seurat_v3') produces scikit-misc error; package not installable with either pip or conda
Question
#3144
by DNApolymerase3
was closed Jul 8, 2024
3 tasks done
OSError between tissue_positions_list.csv and tissue_positions.csv
Bug 🐛
#3085
by alexanderchang1
was closed Jun 7, 2024
2 of 3 tasks
I have always had a question: do I need to scale my adata before running sc.tl.score_genes?
Question
#3080
by christophechu
was closed Jun 7, 2024
3 tasks done
Only show the genes that have significant statistics
Enhancement ✨
#3077
by ngvananh2508
was closed Jun 7, 2024
sc.tl.leiden with Exact replication
Bug 🐛
Needs info❔
More information needed
flavor='igraph' raises an (ignored by igraph) “ValueError: high is out of bounds for int32”
Area – Reproducibility
#3028
by hl324
was closed May 2, 2024
2 of 3 tasks
plots in Rstudio messed up
Area - Plotting 🌺
Bug 🐛
Upstream
#2955
by Sirin24
was closed Apr 3, 2024
2 of 3 tasks
read_10x_mtx() with annData 0.10.4 only reads one variable
Bug 🐛
#2825
by lelandwilliams
was closed Jan 25, 2024
2 of 3 tasks
Something wrong with read_10x_mtx using anndata-0.10.4
Bug 🐛
#2822
by aStudyingTurtle
was closed Jan 23, 2024
2 of 3 tasks
Seaborn throws a FutureWarning when using sc.pl.highest_expr_genes
Bug 🐛
Upstream
#2755
by LinearParadox
was closed Nov 16, 2023
2 of 3 tasks
sc.pp.filter_genes runs out of memory
Needs info❔
More information needed
Question
#2754
by huangdanqi
was closed Nov 16, 2023
2 of 3 tasks
reset sc.pl.DotPlot defaults
Enhancement ✨
Needs info❔
More information needed
#2708
by c-westhoven
was closed Nov 9, 2023
Error running https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html#
Bug 🐛
#2685
by malonzm1
was closed Oct 16, 2023
3 tasks done
PhenoGraph outputs Louvain method when using Leiden
Area – External
Dealing with external tools
Question
#2653
by prubbens
was closed Sep 5, 2023
2 of 3 tasks
sc.tl.rank_genes_groups finds upregulated genes (lfc > 1.5) with pts 0
Bug 🐛
#2628
by noamharel161
was closed Jan 21, 2024
2 of 3 tasks
read_visium() for newer SpaceRanger versions
Enhancement ✨
#2598
by deckerlin
was closed Aug 7, 2023
pl.rank_genes_groups_violin() throws a KeyError when gene_symbols option is passed
Area - Plotting 🌺
Bug 🐛
#2540
by riederd
was closed Jul 7, 2023
2 of 3 tasks
PCA is hanging and taking way too long
Bug 🐛
Needs info❔
More information needed
#2531
by a-munoz-rojas
was closed Jul 7, 2023
2 of 3 tasks
normalize_per_cell raises numpy.core._exceptions.UFuncTypeError
#2500
by scottgigante-immunai
was closed Jun 7, 2023
2 of 3 tasks
sc.pl.spatial TypeError: can't multiply sequence by non-int of type 'float'
Area - IO
Reading and writing
Area – Spatial 🗺
#2499
by meaksu
was closed Jun 26, 2023
PMBC3k tutorial - issue loading saved object from .h5ad file
#2497
by tea-kostic
was closed Jun 7, 2023
2 of 3 tasks
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