GenomicSuperSignature

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How to create new models?

1

Hi, Is it possible to create new models based on `GenomicSuperSignature`? Let's say for example, using `GTEx` as and input and different prior knowledge.

msubirana

Questions about heatmap table function

6

Hi, I found that this step took me a pretty long time to run:  I waited for more than one hour with one 30 GB GPU from an HPC....

HelloWorldLTY

Simplify browsing of studies

2

Currently, looking up which studies contributed to a RAV requires something like the following: ```r > ravc2 colData(ravc2)[colData(ravc2)$RAV == "RAV272", "studies"] $Cl4764_272 [1] "ERP020977" "SRP039361" "SRP045352" ``` And then searching...

lwaldron

PCA is very slow on large single-cell matrices

1

Consider using `irlba` for very large matrices, or allowing use of pre-computed PCA from other packages as input to 1validate()1.

lwaldron

Something like: - https://www.r-bloggers.com/2015/09/passing-arguments-to-an-r-script-from-command-lines/

seandavi

- [x] Spearman - [ ] other methods from dist - [ ] straight function https://github.com/shbrief/GenomicSuperSignature/blob/5e73d06e03f91530e5ae65d25f98ec08dcb056e1/R/validate.R#L15-L37

seandavi

Allow configurable number of PCs in `validate`

1

https://github.com/shbrief/GenomicSuperSignature/blob/5e73d06e03f91530e5ae65d25f98ec08dcb056e1/R/validate.R#L15-L37

seandavi

Release 3 21

1

Updated website rendering on https://bd4everyone.github.io/GenomicSuperSignature/ Thank you

bd4everyone

shbrief

Documentation and user control over PCA

1

The `validate` function and the function it calls `.loadingCor` use the first assay in a SummarizedExperiment to perform PCA. However, many users and standard single-cell workflows perform some kind of...

lwaldron