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epigen
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dea_limma
A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
https://epigen.github.io/dea_limma/
MIT License
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implement contrasts
#29
sreichl
opened
2 days ago
0
Switch pCutoffCol by type of plot (p/adj.p) and fix labels
#28
burtonjake
closed
1 week ago
1
Add numbers to the statistics bar plot
#27
sreichl
closed
6 days ago
1
Error in setwd(snakemake@scriptdir) : cannot change working directory
#26
bednarsky
closed
1 month ago
2
Make clear that annotation.csv can contain multiple rows per analysis
#25
burtonjake
closed
2 months ago
0
Protect aggregate.R from crashing when there are no filtered features.
#24
burtonjake
closed
2 months ago
0
Fix typo in heatmap.R
#23
burtonjake
closed
2 months ago
0
R environment not being set-up
#22
burtonjake
closed
2 months ago
3
Handle empty bed or features_annot.txt
#21
fwzhao
closed
5 days ago
1
use limma's `nonEstimable` and `is.fullrank`
#20
sreichl
opened
2 months ago
0
Generate bed files
#19
fwzhao
closed
2 months ago
1
Revert "Merge with epigen"
#18
fwzhao
closed
2 months ago
0
Merge with epigen
#17
fwzhao
closed
2 months ago
0
eBayes `robust=TRUE`
#16
sreichl
opened
2 months ago
0
map features to genomic regions
#15
sreichl
opened
2 months ago
2
Statistics Barplot breaks in case of no differential features
#14
sreichl
closed
1 week ago
0
Heatmaps do not display most significant value in multi-mapping case
#13
sreichl
opened
3 months ago
0
determine the exact output files from the start for complete compatibility
#12
sreichl
opened
8 months ago
6
consider capping heatmaps
#11
sreichl
closed
7 months ago
1
consider including edgeR 4.0 workflow
#10
sreichl
closed
6 months ago
0
logFC heatmap job does not complete if no DEGs detected
#9
dariarom94
closed
6 months ago
0
support contrasts
#8
sreichl
closed
6 months ago
1
consider saving $E expression matrix that is used in the lmFit linear model
#7
sreichl
closed
6 months ago
0
volcano plot: below indicate absolute LFC being used
#6
sreichl
closed
6 months ago
0
DEA statistics barplot split of up and down by sign
#5
sreichl
closed
6 months ago
0
volcano plots legend has duplicate entries
#4
sreichl
closed
6 months ago
1
add example config, annotation and data
#3
sreichl
opened
1 year ago
0
Snakemake v 7.21 requires output file in rule all
#2
dariarom94
closed
1 year ago
1
configurable gene/feature lists to be plotted as LFC clustered heatmaps and highlighted volcanos (if present)
#1
sreichl
closed
1 year ago
0