Joshua Welch

icon indicating a website link https://medicine.umich.edu/dept/dcmb/joshua-welch-phd icon indicating an email [email protected]

icon location Computational biologist, Associate Professor at University of Michigan, and PI of @welch-lab. We develop novel computational methods for single cell genomics.

Results 7 comments of Joshua Welch

suggestNewK and suggestNewLambda missing in rliger 1.0.0?

The functions you’re looking for are optimizeNewK and optimizeNewLambda. On Oct 7, 2021, at 9:28 PM, Chao Gao ***@***.***> wrote:  External Email - Use Caution Hi, you might refer...

Integrate multiomics RNA and ATAC data generates trivial all-zero latent values

Do you mean that some cells have iNMF factor loadings that are identically 0 for all factors? — Joshua D. Welch, Ph.D. Assistant Professor Department of Computational Medicine and Bioinformatics...

scRNAseq Integration with CODEX Data

We haven’t tried liger on codex, but it should work in principle. If you try it, you may want to check out the UINMF algorithm that April has developed. It’s...

Treating scRNAseq results as bulk RNAseq

If you just want to find DE genes between all cells from each condition, you can assign all cells to a single "dummy" cluster and use runWilcoxon by dataset. ________________________________...

recovering expression for differential analysis

The way we do DE gene analysis is (1) find joint clusters using LIGER and (2) perform Wilcoxon rank-sum test between datasets within each joint cluster. This relies on an...

Question re: root cells in latent time / velocity streams

One other suggestion is to look carefully at the selected genes. If there are batch effects, the highly variable genes may be more related to the batch differences than the...

Continuous pancreas notebook not reproducible

To clarify, Yichen only tested the model on single-precision GPUs. Moving to double precision on CPU likely changes when the early stopping criterion is triggered or something about the relative...