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markziemann
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mitch
An R package for multi-dimensional pathway enrichment analysis
https://bioconductor.org/packages/mitch
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handling pvalues of zero causes infinites in edgeR
#41
markziemann
opened
1 month ago
1
Remove redundant sets
#40
markziemann
opened
2 months ago
0
Fix the warnings for methylation data
#39
markziemann
opened
2 months ago
0
Pre-filtering of results?
#38
dakota-hawkins
closed
6 months ago
2
Make sure prescored works properly with methylation data
#37
markziemann
closed
6 months ago
0
Regenerate the docs to indicate the change in CPU usage.
#36
markziemann
closed
7 months ago
1
Check that kableExtra tables are being created properly in the detailed results
#35
markziemann
closed
7 months ago
2
announce changes
#34
markziemann
closed
9 months ago
0
default of cores should be 1
#33
markziemann
closed
7 months ago
1
Problem when importing a single dataframe with prescored data
#32
markziemann
closed
1 year ago
1
Error in names(y) %in% geneIDcol
#31
dkmadsen
closed
7 months ago
2
Edge case error where contrasts are replicated
#30
markziemann
closed
7 months ago
1
Rmarkdown report chunk headers
#29
markziemann
closed
1 year ago
0
Q: should I apply a cut off when importing DEGs
#28
Pstege
closed
2 years ago
1
Enrichment of very simillar samples
#27
fisst
closed
2 years ago
1
change variable name in melted data frames for HTML and PDF outputs
#26
matt-sd-watson
closed
2 years ago
4
mitch_import error when using Seurat v4
#25
tjbencomo
closed
2 years ago
1
if there are no statisticaly significant pathways, then the 1d analysis HTML fails
#24
markziemann
closed
7 months ago
1
Need to start part 2
#23
markziemann
closed
3 years ago
0
Create a bubble plot for unidimensional analysis
#22
markziemann
opened
3 years ago
1
Question on Type I Error
#21
gabrielodom
closed
2 years ago
8
spaces in colnames causes an error in ggpairs/ggcontour plot
#20
markziemann
closed
7 months ago
0
gmt_import problem with empty lines
#19
markziemann
closed
7 months ago
1
Turn off pbmclapply
#18
markziemann
closed
4 years ago
0
saveRDS is more efficient
#17
markziemann
closed
4 years ago
0
Error in sparse matrix
#16
markziemann
closed
4 years ago
1
Check that special characters in the colnames don't break the reports and plots
#15
markziemann
closed
4 years ago
1
Check that the gene sets are not duplicated
#14
markziemann
closed
4 years ago
0
mitch_report fails if an absoulte path is given as outfile
#13
Christian-Heyer
closed
4 years ago
3
Error when running several DE genes per cluster
#12
ccruizm
closed
4 years ago
13
Rmd first plot for 2d analysis
#11
markziemann
closed
4 years ago
1
Output file naming mitch_report()
#10
HeyLifeHD
closed
4 years ago
4
Problem with the interactive charts
#9
markziemann
closed
4 years ago
2
Lots of warnings in the vignette
#8
markziemann
closed
4 years ago
1
NAs present in test statistics
#7
markziemann
closed
4 years ago
0
Use GSEABase to import genesets
#6
markziemann
closed
4 years ago
0
Import prescored data
#5
markziemann
closed
5 years ago
0
NA handling bug in unidimensional analysis
#4
markziemann
closed
5 years ago
1
R manova limit
#3
markziemann
closed
5 years ago
0
Import from more single cell packages in bioconductor
#2
markziemann
closed
5 years ago
4
Replace taucharts with echarts4r
#1
markziemann
closed
5 years ago
1