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"

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Subclustering

#65 lu77777777 closed 3 years ago
4
visualization for UMAP error

#64 lu77777777 closed 3 years ago
0
%%R -i data_mat -i input_groups -o size_factors size_factors = computeSumFactors(data_mat, clusters=input_groups, min.mean=0.1)

#63 lu77777777 closed 3 years ago
3
R language in .py file

#62 lu77777777 closed 3 years ago
1
AttributeError: module 'louvain' has no attribute 'set_rng_seed'

#61 lu77777777 closed 3 years ago
1
%%R -i data_mat -i input_groups -o size_factors

#60 allisoncheney closed 3 years ago
3
can't set up environment

#59 JuanTan628 closed 3 years ago
9
Notebook update to January 2021 version

#58 LuckyMD opened 3 years ago
3
ValueError: cannot reindex from a duplicate axis

#57 Leran10 closed 3 years ago
10
no latest tag for Docker container

#56 Zethson closed 3 years ago
2
normalization: scran vs neg. binomial regression (sctransform)

#55 grst closed 3 years ago
7
Add missing files for docker container building

#54 le-ander opened 3 years ago
17
Make concat function call compatible with updated scanpy

#53 lzhus closed 3 years ago
3
sc.pp.neighbors(adata_pp)

#52 mabaoweireadingene closed 3 years ago
2
Building container image failes due to missing files

#51 serverhorror closed 1 year ago
8
InvalidIndexError: Reindexing only valid with uniquely valued Index objects

#50 814471489 closed 3 years ago
4
%%R -i data_ent

#49 hatuyen4994 opened 4 years ago
21
adata.concatenate

#48 mabaoweireadingene closed 4 years ago
4
Update dockerfile

#47 le-ander closed 4 years ago
1
Add Dockerfile for sc-analysis Container

#46 le-ander closed 4 years ago
0
Dockerfile is not visible

#45 serverhorror closed 4 years ago
8
concatenation issue persists after commenting out two lines as instructed in issue #41

#44 SuhanG17 closed 4 years ago
4
Problems when installing package"Slingshot"and "Monocle"

#43 satellite119 closed 4 years ago
8
Kernel restarting when concatenating

#42 omanor closed 3 years ago
3
Problem with adata concatenation

#41 davidtourigny closed 4 years ago
12
computeSumFactors(data_mat, clusters=input_groups, min.mean=0.1) gives error

#40 ariberar closed 4 years ago
16
mt fraction calculation

#39 giovp closed 3 years ago
2
Different outputs

#36 evenDDDDD closed 3 years ago
3
Best practices for using regress_out?

#35 oligomyeggo closed 4 years ago
11
adata.var['gene_id-1']

#34 yuGithuuub closed 4 years ago
0
TypeError: Callable[[arg, ...], result]: each arg must be a type. Got Ellipsis.

#33 jjaa-mp closed 4 years ago
1
Issues with sc.pp.highly_variable_genes following tutorial

#32 oligomyeggo closed 4 years ago
3
Error on "Making variable names unique for controlled concatenation."

#31 aheravi closed 4 years ago
1
scanpy.plotting.palettes' has no attribute 'default_64

#30 f6v closed 4 years ago
1
ComBat Error

#29 Zifeng-L closed 4 years ago
6
Exception: Data must be 1-dimensional when plotting new marker genes in jupyter notebook

#28 federicaress closed 4 years ago
15
Problem correcting batches with Combat

#27 ccruizm closed 4 years ago
5
Error in samples concatenation

#25 ParisaMa closed 5 years ago
2
R libraries not accessible

#24 mumichae closed 3 years ago
17
Get environment setup info

#23 mbuttner closed 5 years ago
1
Error in differential expression analysis

#22 Vyoming closed 5 years ago
1
Key error with gene_id-1

#21 Vyoming closed 5 years ago
5
MAST returns natural log, not log2FC

#20 le-ander closed 3 years ago
3
Fixed folder name

#19 federicomarini closed 5 years ago
9
Concatenate files error

#18 davidepisu closed 4 years ago
22
Unable to deploy the .yml - Docker enhancement request

#17 marshelma closed 3 years ago
11
cleaner typo fix

#16 ttriche closed 5 years ago
1
fix typo

#15 ttriche closed 5 years ago
1
sc.tl.marker_gene_overlap error

#14 JuHey closed 5 years ago
3
Issue with rgl package when trying to load slingshot

#13 brennerUT closed 5 years ago
7

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