theislab / single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

theislab/single-cell-tutorial Issues

creating the env in windows
Updated 4 months ago
sc.tl.rank_genes_groups , p value question
Updated 5 months ago1
AttributeError: module 'pertpy.tools' has no attribute 'Milopy'
Closed 9 months ago2
Package versions in .yml file
Closed 3 years ago10
Concatenating issue when plotting analytic_pearson_residuals layers
Updated a year ago7
ValueError: Unknown dtype dtype('uint16') cannot be converted to ?gRMatrix.
Updated a year ago4
Scale before calculating gene score, and after regressing out cell cycle ?
Closed 2 years ago2
environment installation problem
Updated a year ago1
enviroment install failed
Updated 2 years ago1
Sparse matrix dimensions
Updated 2 years ago1
sc.tl.rank_genes_groups and pct1 & pct2 output
Closed 2 years ago1
Batch correction with combat causes Jupyter kernel to die
Closed 2 years ago2
Can we also use Seurat v3 v4 or liger in scanpy or python?
Closed 2 years ago7
concatenate to main adata object
Closed 2 years ago1
List of package versions for the latest version of the notebook
Closed 2 years ago3
executing sc.tl.rank_genes_groups() function on tutorial data provides incorrect results
Closed 2 years ago1
How can we change the plot shape (not only using dot) of UMAP in Scanpy?
Closed 2 years ago2
get the clustering and subclustering results differ from those given in example
Closed 2 years ago
Key Error "base" in section "marker genes & annotation"
Closed 2 years ago4
R command throw UnicodeDecodeError
Updated 2 years ago3
Batch correction runtime warning: Divide by zero
Closed 2 years ago6
Too few Duodenum cells
Closed 2 years ago1
Error
Closed 2 years ago1
FileNotFoundError: [Errno 2] No such file or directory: '../Macosko_cell_cycle_genes.txt'
Closed 2 years ago2
Damaged tar archive
Closed 2 years ago2
Normalizing subsetted data
Updated 2 years ago1
Interpretation of rank_genes_groups
Closed 2 years ago1
ValueError: cannot reindex from a duplicate axis
Closed 3 years ago7
RRuntimeError: Error in validObject(.Object) :
Updated 2 years ago1
searborn.distplot() is deprecated
Updated 2 years ago1
Reference for downloading the dataset
Updated 2 years ago1
(Report a problem) Cannot reindex from a duplicate axis
Closed 3 years ago8
combine clusters after clustering
Closed 2 years ago1
numpy.core._exceptions.MemoryError: Unable to allocate 926. GiB for an array with shape (6794880, 36601) and data type float32
Closed 2 years ago1
clustering resolutions--how to tune
Closed 2 years ago3
Running in pure python env: in a .py file
Updated 3 years ago1
ValueError: 'Enterocyte mature' is not a valid category for 'louvain_r0.5_entero_sub'
Updated 3 years ago1
TypeError when trying to add known marker genes
Closed 3 years ago7
Choice of gene sets for cell cycle scoring
Updated 3 years ago1
computeSumFactors run error (Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"matrix", "character"’)
Closed 3 years ago7
louvain vs leiden
Closed 3 years ago2
What type of matrix should `score_genes` be applied to?
Updated 3 years ago
Resetting Max Buffer Size for Jupyter Notebook
Closed 3 years ago5
Cannot open jupyter lab in docker container
Closed 3 years ago1
Is it necessary to specify `n_genes` in box 35
Closed 3 years ago1
Error in dataloader
Closed 3 years ago7
Subclustering
Closed 3 years ago4
visualization for UMAP error
Closed 3 years ago
%%R -i data_mat -i input_groups -o size_factors size_factors = computeSumFactors(data_mat, clusters=input_groups, min.mean=0.1)
Closed 3 years ago3
R language in .py file
Closed 3 years ago1