MPAL-Single-Cell-2019 issues

Runtime of getting UMAP reductions

4

I am trying to run `scRNA_01_Clustering_UMAP_v1.R`, and apparently the function `optimizeLSI` is iterative. The code shows that each iteration take 30 seconds and the maximum number of iterations is 3000....

mohit1997

Cell barcode IDs for processed ATAC SummarizedExperiment objects

Hi, Many thanks for the repository of code and data. I was hoping to use some of the healthy scATAC datasets, but after downloading the healthy hematopoiesis scATAC cell x...

andrewjkwok

scRNA cell type annotation marker

1

Hi, can you share me the markers you used for scRNA-seq cell cell type annotation.Thanks.

dhoneyi

Label transfer from RNA to ATAC

Hi @jgranja24 @jeffmgranja I had a question regarding this sentence from the methods section: "Matching scATAC-seq-scRNA-seq pairs using Seurat’s canonical correlation analyses. To integrate our epigenetic and transcriptomic data we...

RegnerM2015

Antibody features in raw 10x Bam Files provided in the repository link

Thank you for freely providing these datasets and analysis scripts. I've tried to recover the gene expression and antibody features data from an original 10X bam file (sample GSM4138874) and...

GAgafencu

Where is the bam file for scATAC-seq data?

6

Can you tell me How can I download the bam file for scATAC-seq data? Thanks!

eravza

Code for creating differentiual_Summary objects is missing

1

I went through your pipeline and the part that is producing the first two input files for scRNA_scATAC_Integration_04_Link_TFs_To_Targets.R script is missing. Could you please clarify about this part futher? ```...

CSBioAzim