10x-scATAC-2019

10x-scATAC-2019 copied to clipboard

Do you have the file just like this ? This is the Cicero hematopoiesis datasets from your work. The author of paper "Combining SNP-to-gene linking strategies to identify disease genes...

zhouxiaohong15

Hi, I really appreciate your work on scATAC-seq. I tried to run GWAS chromVAR on single-cell summarized experiment using co-accessibility. However, I was unable to find the dataset of PICS_GWAS_SNPS.gr.rds....

Sophiesze

Was just wondering if someone might be able to comment on what changes would be needed to adapt the 05_Cluster_Unique_Peaks_v2.R script to make it appropriate for detecting unique gene activities,...

owenwilkins

Hi, I am trying to access some public data from your paper and I followed the instructions of "Getting 10x scATAC-seq Bam Files" in README. In the final figure of...

eravza

NO fragments.tsv.gz OF Hematopoiesis cells

1

Hi, I have downloaded scATAC_Heme_All_SummarizedExperiment.final.rds followed your links. I checked the ```Group``` information in ```colData```. And I also want to use the segments files from this cells. ``` table(Heme_meta_info$Group) B_Cells...

pangxueyu233

Hi, I am trying to get the public data of your paper and I followed the instructions of "Getting 10x scATAC-seq Bam Files" in README. However I failed to find...

Aelita-Stone

Hi, I'm an ArchR user that was directed to this repository to perform CNV Analysis since the feature is not yet available in ArchR. I have a few questions about...

hugokitano

02

8

Making Seurat LSI Object... Binarizing matrix... Getting top 20000 features... Computing Term Frequency IDF... Computing SVD using irlba... Making Seurat Object... Error in CreateSeuratObject(mat, project = "scATAC", min.cells = 0,...

hjack123

Hi, Thanks for your great works and sharing your code. When I use your analyze the umap trajectory code to construct the trajectory in my own data, I have some...

dhoneyi

Hi, I am rerunning your human-mouse cell mixture data, but I cannot find a proper list to use for gene.ranges and tss.ranges. Could you share with me how you find...

mailcolm9