theislab single-cell-tutorial issues

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"

1.35k stars 448 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

creating the env in windows

#115 Mehrr11 opened 7 months ago
0
sc.tl.rank_genes_groups , p value question

#114 ruiqiizhou opened 7 months ago
1
Concatenating issue when plotting analytic_pearson_residuals layers

#113 ngvananh2508 opened 1 year ago
7
AttributeError: module 'pertpy.tools' has no attribute 'Milopy'

#112 nroak closed 1 year ago
2
ValueError: Unknown dtype dtype('uint16') cannot be converted to ?gRMatrix.

#111 nroak opened 1 year ago
4
environment installation problem

#110 Sunyp-IM opened 1 year ago
1
Add content warning to README

#109 Zethson closed 1 year ago
2
enviroment install failed

#108 Sunyp-IM opened 1 year ago
1
concatenate to main adata object

#107 Yuling-Zhao closed 1 year ago
1
Update installation manual

#106 mbuttner opened 1 year ago
3
Sparse matrix dimensions

#105 acihanckr opened 1 year ago
1
List of package versions for the latest version of the notebook

#104 davidecarlson closed 2 years ago
3
Scale before calculating gene score, and after regressing out cell cycle ?

#103 carmensandoval closed 1 year ago
2
executing sc.tl.rank_genes_groups() function on tutorial data provides incorrect results

#102 Monkeyninjaw closed 2 years ago
1
How can we change the plot shape (not only using dot) of UMAP in Scanpy?

#101 melancholy12 closed 2 years ago
2
get the clustering and subclustering results differ from those given in example

#100 imemorizedpi closed 2 years ago
0
sc.tl.rank_genes_groups and pct1 & pct2 output

#99 TRakesh0121 closed 1 year ago
1
Can we also use Seurat v3 v4 or liger in scanpy or python?

#98 melancholy12 closed 1 year ago
7
Key Error "base" in section "marker genes & annotation"

#97 Mari123i closed 2 years ago
4
Batch correction with combat causes Jupyter kernel to die

#96 barbareyex closed 1 year ago
2
R command throw UnicodeDecodeError

#95 Mari123i opened 2 years ago
3
Too few Duodenum cells

#94 Mari123i closed 2 years ago
1
Error

#93 skr3178 closed 2 years ago
1
FileNotFoundError: [Errno 2] No such file or directory: '../Macosko_cell_cycle_genes.txt'

#92 skr3178 closed 2 years ago
2
Damaged tar archive

#91 sudoyang closed 2 years ago
2
Normalizing subsetted data

#90 oligomyeggo opened 2 years ago
1
Interpretation of rank_genes_groups

#89 Lavieenrose123 closed 2 years ago
1
Reference for downloading the dataset

#88 Sangram-Rout opened 2 years ago
1
combine clusters after clustering

#87 DUAN-GAO closed 2 years ago
1
clustering resolutions--how to tune

#86 DUAN-GAO closed 2 years ago
3
numpy.core._exceptions.MemoryError: Unable to allocate 926. GiB for an array with shape (6794880, 36601) and data type float32

#85 DUAN-GAO closed 2 years ago
1
searborn.distplot() is deprecated

#84 le-ander opened 2 years ago
1
Running in pure python env: in a .py file

#83 DUAN-GAO opened 2 years ago
1
ValueError: cannot reindex from a duplicate axis

#82 DUAN-GAO closed 2 years ago
7
RRuntimeError: Error in validObject(.Object) :

#81 vincentxu199112 opened 2 years ago
1
ValueError: 'Enterocyte mature' is not a valid category for 'louvain_r0.5_entero_sub'

#80 vincentxu199112 opened 2 years ago
1
Batch correction runtime warning: Divide by zero

#79 dturaev closed 2 years ago
6
Choice of gene sets for cell cycle scoring

#78 fbnrst opened 2 years ago
1
Add fixes for 2021 container

#77 Zethson opened 2 years ago
4
TypeError when trying to add known marker genes

#76 oligomyeggo closed 2 years ago
7
louvain vs leiden

#75 oligomyeggo closed 3 years ago
2
Package versions in .yml file

#74 lefterov closed 3 years ago
10
What type of matrix should `score_genes` be applied to?

#73 liuzj039 opened 3 years ago
0
Resetting Max Buffer Size for Jupyter Notebook

#72 JakeLehle closed 3 years ago
5
Error in dataloader

#71 wiedemer closed 3 years ago
7
Is it necessary to specify `n_genes` in box 35

#70 yugeji closed 3 years ago
1
Update sc_tutorial_environment.yml

#69 herokoking closed 3 years ago
1
Cannot open jupyter lab in docker container

#68 dong7422 closed 3 years ago
1
(Report a problem) Cannot reindex from a duplicate axis

#67 Teerapon789 closed 3 years ago
8
computeSumFactors run error (Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"matrix", "character"’)

#66 rdcwuyy closed 3 years ago
7