claassenlab MORESCA issues

claassenlab / MORESCA

This repository provides a template and some resources on standardized scRNA-seq analysis using Python.

GNU Affero General Public License v3.0

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Allow specifying a layer for differential expression testing

#58 janschleicher opened 9 months ago
0
Add default values for arguments of all analysis steps. Closes #56.

#57 janschleicher closed 9 months ago
1
Default values for function arguments

#56 janschleicher closed 9 months ago
1
Fixed semi-automatic selection for n_comps in PCA

#55 mbruhns opened 11 months ago
0
Reduce size of test data

#54 Baschdl opened 11 months ago
0
Remove hardcoded use_raw=True from sc.pl.rank_genes_groups in diff_gene_exp

#53 janschleicher closed 11 months ago
1
Differential expression should use raw only if specified as argument

#52 janschleicher closed 11 months ago
0
ddqc thresholding

#51 mbruhns opened 11 months ago
0
More tests needed

#50 janschleicher opened 11 months ago
0
Quality control currently does not remove cells or genes

#49 janschleicher closed 11 months ago
0
Find a better way to store config parameter values in `adata.uns` if `apply==None`

#48 janschleicher opened 11 months ago
0
Change DGE default from raw to count layer.

#46 mbruhns closed 11 months ago
1
Switch to ruff

#45 mbruhns opened 11 months ago
0
Run UMAP on original or PCA transformed data

#44 Baschdl opened 11 months ago
1
26 implement plotting function

#43 janschleicher closed 11 months ago
1
14 auto mode for qc

#42 mbruhns closed 11 months ago
0
Add docstrings, run black.

#41 mbruhns closed 11 months ago
1
Add X_pca_corrected layer if harmony is run; closes #18.

#40 janschleicher closed 11 months ago
0
Add docstring into codebase

#39 mbruhns closed 11 months ago
0
Fix formatting error for installation of dev mode.

#38 mbruhns closed 11 months ago
1
Make diff_gene_exp use layer instead of raw

#37 janschleicher closed 11 months ago
0
Test validity of config file

#36 Baschdl opened 11 months ago
1
16 modification of saving scheme

#35 janschleicher closed 11 months ago
1
Stable clustering alternative

#34 mbruhns opened 11 months ago
1
Add explicit specification of code location for setuptools

#33 Baschdl closed 11 months ago
1
"dev" mode doesn't exist in pyproject.toml

#32 Baschdl closed 11 months ago
1
24 allow users to specify a single value or a range of values for clustering

#31 mbruhns closed 11 months ago
1
Remove saving in individual steps

#30 mbruhns closed 11 months ago
1
Add pynndescent to dependencies.

#29 mbruhns closed 11 months ago
0
Gene removal

#28 janschleicher closed 11 months ago
1
Add metric parameter for neighborhood_graph.

#27 mbruhns closed 11 months ago
1
Implement plotting function

#26 mbruhns closed 11 months ago
0
Consider the feasibility of hierarchical clustering

#25 mbruhns opened 11 months ago
0
Allow users to specify a single value or a range of values for clustering

#24 mbruhns closed 11 months ago
0
Parameter selection for Leiden clustering

#23 mbruhns opened 11 months ago
0
Explore elbow estimation techniques as detailed in relevant literature

#22 mbruhns opened 11 months ago
0
Selection of number of PCs

#21 mbruhns opened 11 months ago
0
Include the pynndescent package

#20 mbruhns closed 11 months ago
0
Metric option in neighbors function

#19 mbruhns closed 11 months ago
0
Layer for X_pca_corrected values

#18 mbruhns closed 11 months ago
0
Log of anomalous values

#17 mbruhns opened 11 months ago
0
Modification of saving scheme

#16 mbruhns closed 11 months ago
0
Implement UMAP plotting following pre-processing

#15 mbruhns opened 11 months ago
0
Auto mode for QC

#14 mbruhns closed 11 months ago
0
Integrate into nf-core pipeline

#13 mbruhns opened 1 year ago
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Add correction of ambient RNA

#12 mbruhns opened 1 year ago
0
changed hemoglobin regex to exclude HBEGF and HBS1L

#11 janschleicher closed 1 year ago
2
Genes should only be removed after normalization

#10 janschleicher closed 11 months ago
0
Download 3kPBMC data set in Github action

#9 mbruhns opened 1 year ago
0
Working example

#8 Baschdl opened 1 year ago
0