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`scale` parameter is missing in `degPCA`

1

There is no parameter in `degPCA` to pass `scale` to `prcomp` function, which means the data is not scaled during PCA. However, scaling the data before PCA is often suggested.

bounlu

degCovariates does not shade by r value

5

degCovariates produces a graph and outlines significant results, but does not actually shade graph based on r correlation value. This is despite R values being non-zero. I tried replacing the...

hwick

How does degPatterns() decide what height to use for cutting tree

1

Hi Lorena, Thank you for providing this great package! I am just wondering how does `degPatterns()` decide what height to use for cutting the tree? And is there a way...

sang-15

issues with degPatterns not setting Time in Normalize

8

First my versions: OSX latest R version: [1] dplyr_1.1.1 tibble_3.2.1 plyr_1.8.8 [4] cluster_2.1.4 edgeR_3.40.2 limma_3.54.2 [7] DEGreport_1.34.0 pheatmap_1.0.12 ggplot2_3.4.2 [10] DESeq2_1.38.3 SummarizedExperiment_1.28.0 Biobase_2.58.0 [13] MatrixGenerics_1.10.0 matrixStats_0.63.0 GenomicRanges_1.50.2 [16] GenomeInfoDb_1.34.9 IRanges_2.32.0...

kesner

Boxplot position

1

Hi there, Firstly, thanks for developing this wonderful tool to visualize trends. I'm wondering if the function can re-position the boxplot in the same line(the blue line in the graph)...

Chunhuixu

Connecting dots and lines in degPlotCluster()

1

Hello, Thanks for your amazing tool! I have a very mild issue regarding the degPlotCluster() function. When I use the function with the option color = "cell_state" for example, the...

CroixJeremy2

how to change color in degPlotCluster()

1

 I have a problem on changing the color of the figure made by "degPlotCluster". like this figure. my control is shown in red color, my treatment is colored in...

zhaodebiao5385