Lucy Garner

`reduce_dimensionality` on expression matrix filtered for highly variable genes?

1

Hi, I was wondering whether you had compared SCORPIUS results using either the expression matrix for all genes or an expression matrix filtered for highly variable genes as input to...

Error in array(ans, c(len.a%/%d2, d.ans), if (!is.null(names(dn.ans)) || : negative length vectors are not allowed

1

Hi, I am getting this error at the `extract_modules` step, which appears to be related to the maximum length of allowed vectors in R: https://stackoverflow.com/questions/42479854/merge-error-negative-length-vectors-are-not-allowed, https://github.com/alyssafrazee/polyester/issues/41, https://support.bioconductor.org/p/66401/ > "You are...

Hi, I was wondering whether you have compared using all genes vs. only highly variable genes (HVGs) as input for the multi-dimensional scaling step? The reason I ask is that...

Expected the fold change column in the `FindAllMarkers` output data.frame to be named `avg_diff` when using the "scale.data" slot, but it is named `avg_log2FC`. ```r library(Seurat) library(SeuratData) InstallData("pbmc3k") data("pbmc3k") pbmc3k...

Segmentation fault with `DiffusionMap`

4

Hi, I am getting a segmentation fault with `DiffusionMap`. I am not changing any of the defaults. 1) When inputting a data matrix as `data`, I get the following error:...

Number of cell types required

1

How many cell types are required for haystack_bio to provide accurate and reliable results? For example, I have ATAC-seq and RNA-seq data on three cell types? Would this be sufficient...

Hi @kassambara, I am getting slightly different p-values if I `p.adjust.method` within `wilcox_test` or run `p.adjust` afterwards and I am just trying to understand why. ``` data(iris) iris$Petal.Width % wilcox_test(Sepal.Length...

Issue accessing www.celltypist.org - 502 Bad Gateway

3

Hi, I am getting the following error when trying to access www.celltypist.org.  Are others having this issue as well? Best wishes, Lucy

Gini coefficient

3

Hi, I was wondering whether there is a function inside vegan for calculating the Gini coefficient, as this is another diversity metric that is used a lot for TCR/BCR repertoire...

Implement bootstrapCluster for clusters generated in Seurat

6

Hi, I would like to establish the stability of the clusters that I have identified using Seurat (FindNeighbors and FindClusters). I was wondering how difficult it would be for me...