Anjali Chawla
Anjali Chawla
Hi, thanks for this truly awesome tool. As you may already know, there is a lot of discussion around using which parameters for MACS2 peak calling in single-nucleus ATAC-seq. I...
Hi, Thanks for this very cool tool! Could you please suggest a way to determine sex of every sample in vcfR? One approach I know is heterozygosity rate on chrX....
Hi, Is there a way to make demultiplexing procedure any faster? Even with 32 cpus and 200g mem - it takes 2 days to finish for a 30g fastq files....
plotGroups(proj,colorBy="GeneIntegrationMatrix", name="PLP1", groupBy="Clusters", plotAs="violin",threads=1) Error: Getting ImputeWeights No imputeWeights found, returning NULL 2022-10-14 19:54:41 : Getting Matrix Values... 1 2 3 4 5 6 7 8 9 10
Hi @rcorces, I tried using this approcah but ended up with this error: devtools::install_github("GreenleafLab/ArchR", ref="dev", repos = BiocManager::repositories()) proj
Hi, CellSNP-lite works well for most of my data except this bam file where it throws the following error. Please let me know what is causing this error and how...
Hello, I have 2 pooled snATAC donors and their individual bulk RNA-seq data. To demultiplex, my strategy was to call common variant SNPs for the two individuals separately using CellSNP,...
Hi, can you please let me know if my understanding is correct in this issue. Thank you!!! https://github.com/HelenaLC/muscat/issues/102#issue-1203975480
Hi, In resDS function - you calculate cpm from y$data[[k]] .This will work for edgeR as this returns normalized count but will not work when using limma-voom. - as.matrix(y$data[[k]]) returns...
Hi, Thank you for this great package. I am using Deseq2 mthod with pbDS function and got this error: Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at...