issues
search
ktrns
/
scrnaseq
Workflow for single-cell RNA-seq analysis using Seurat
MIT License
37
stars
15
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Implementation of a more general DEG analysis
#67
andpet0101
closed
3 years ago
1
in case of few cells error in Seurat::RunPCA
#66
dimialex
closed
3 years ago
1
qc_plot_cells does not work for samples with less than three cells
#65
andpet0101
closed
3 years ago
0
Small issues to change in the main script
#64
ktrns
closed
3 years ago
0
DegsAvgData mean calculation
#63
andpet0101
closed
3 years ago
1
Export figures to PDF
#62
ktrns
closed
3 years ago
0
Update code after major changes in cerebroApp
#61
andpet0101
closed
3 years ago
0
Documentation of code
#60
ktrns
opened
3 years ago
1
Simplify structure
#59
ktrns
closed
3 years ago
0
future framework warnings about not statistically sound random seeds
#58
dimialex
closed
3 years ago
0
Update of MHH-RCUG/scrnaseq (master) with ktrns/scrnaseq (master)
#57
tglomb
closed
3 years ago
1
HTO normalisation advice
#56
andpet0101
closed
3 years ago
10
Integration versus merging, CellCycleScoring on individual samples or merged dataset?
#55
ktrns
closed
3 years ago
4
Authors of the scrnaseq workflow
#54
ktrns
closed
2 years ago
1
PR to merge branch updatePlots into master
#53
ktrns
closed
4 years ago
0
Reintegration of violin plots
#52
tglomb
closed
4 years ago
0
Seurat FindAllMarkers uses natural log to calculate FC, we'd like to have log2
#51
ktrns
closed
4 years ago
0
Some (sub-)panels (e.g. of ridge plot, violin plot) get strongly compressed the more clusters were identified
#50
Oliver-D-B
closed
4 years ago
2
Mhh rcug start script with parameters from outside for hto
#49
ktrns
closed
4 years ago
0
Cerebro support
#48
andpet0101
closed
4 years ago
0
scrnaseq shiny app
#47
mariusrueve
closed
3 years ago
0
Pseudotime analysis
#46
ktrns
opened
4 years ago
3
DEGs between multiple samples
#45
ktrns
closed
3 years ago
1
Identified celltype-specific markers are sometimes misleading due to current selection criteria
#44
Oliver-D-B
closed
3 years ago
5
Even more explanatory / introductory texts for unexperienced users
#43
Oliver-D-B
closed
2 years ago
6
Problem with the dot plot panel if the same gene serves as TOP candidate for two clusters
#42
Oliver-D-B
closed
4 years ago
0
Output of functional enrichment results is not informative yet
#41
Oliver-D-B
closed
4 years ago
2
(Re)Integration of the violin plots
#40
Oliver-D-B
closed
4 years ago
3
Consistency in filter criteria and order of marker genes needs improvement
#39
Oliver-D-B
closed
4 years ago
4
We need to rename cells if we integrate several datasets
#38
ktrns
closed
4 years ago
0
Clarify the difference between DEGs and markers
#37
ktrns
closed
4 years ago
0
Start script with parameters from outside for hto
#36
tglomb
closed
4 years ago
2
Double-check translation of gene names in reading function
#35
ktrns
closed
4 years ago
0
Support of multiple samples
#34
andpet0101
closed
4 years ago
3
Known features and issue fixes
#33
ktrns
closed
4 years ago
0
Check parameters at the start
#32
andpet0101
closed
3 years ago
2
Can we add expression values to the output in markers.xlsx?
#31
ktrns
closed
3 years ago
0
DEG output table markers.xlsx lacks annotation
#30
ktrns
closed
4 years ago
0
Merge changes regarding HTO script usage with parameters from outside the script.
#29
tglomb
closed
4 years ago
5
Start script with parameters from outside for hto
#28
tglomb
closed
4 years ago
0
Allow more possibilities for gene name conversion
#27
andpet0101
closed
3 years ago
0
Small fixes
#26
ktrns
closed
4 years ago
0
Check online ressources at the start
#25
andpet0101
closed
4 years ago
6
Read and plot known marker genes from file
#24
ktrns
closed
4 years ago
2
Singularity container trial
#23
colindaven
closed
4 years ago
7
Remove cell cycle effects
#22
ktrns
closed
4 years ago
0
Improve feature plots for known marker genes
#21
ktrns
closed
4 years ago
1
Read simple expression matrix as input
#20
ktrns
closed
4 years ago
5
HTML tables appear as full width even though full_width=FALSE
#19
ktrns
closed
4 years ago
0
Print versions at the end of report
#18
ktrns
closed
4 years ago
3
Previous
Next