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View Code? Open in Web Editor NEWA Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
License: MIT License
A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
License: MIT License
only implement if a use case is presented.
Implement automatic DEA comparison of all pairs within a metadata label.
Annotation column control could be "PAIRWISE" or "PAIRS"
To get a better overview of the number of differential features in each direction(!), up and down, the barplot could go literally up and down from zero. "down" features need a negative sign (-).
plot_df are the DEA statistics.
# plot config
direction_col <- list("up"="red", "down"="blue")
# plot
ggplot(plot_df, aes(x=groups, y=n_features, fill=direction)) +
geom_bar(stat="identity", position="identity") +
scale_fill_manual(values=direction_col) +
custom_theme +
theme(legend.position = "none",
axis.text.x = element_text(angle = 45, vjust = 1, hjust=1)
)
only implement if a use case is presented.
neg. binomial tests use the following parameters, which are currently hard-coded (to default) or not supported:
feature_lists: ALL, ...
Consider: it is a breaking change as it requires a new config field...
same functionality as implemented in dea_limma module.
If only two cell groups are provided, there is only one column in the pheatmap plot (heatmap.R) and hclust causes an error.
This fixes it:
clusterCols <- ncol(dea_lfc) > 1
lfc_heatmap <- as.ggplot(pheatmap(dea_lfc,
show_rownames=F,
show_colnames=T,
cluster_cols = clusterCols,
fontsize = 5,
angle_col = 45,
treeheight_row = 25,
treeheight_col = 10,
breaks=seq(-max(abs(dea_lfc)), max(abs(dea_lfc)), length.out=200),
color=colorRampPalette(c("blue", "white", "red"))(200),
annotation_names_col = F,
silent = TRUE
))
this is important to be used eg for correction in enrichment analyses (eg as background gene set)
setup Lee2020NatGenet as example data.
Hello,
thanks for the effort to turn the Seurat pipeline into a snakemake.
The following line in the Snakefile gives me an error since the function srcdir is not defined:
SDIR = os.path.realpath(os.path.dirname(srcdir("Snakefile")))
Had to comment it out to get to to run.
cheers
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