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theislab
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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"
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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
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