Lucy Garner

`RunHarmony` - Warning: Invalid name supplied, making object name syntactically valid

2

Hi, I am running harmony as follows: ``` seurat_object

Error in `dplyr::select()`: ! <text>:1:5: unexpected symbol

4

Hi, I am getting the following error when I run `RunHarmony` on my Seurat object and I can't work out where this `dplyr::select()` is coming from. `seurat_object Error in `dplyr::select()`:...

Integrating SCTransform-normalised data with LIGER

1

Related to #161, is it still necessary to manually ensure that the Pearson residuals are non-negative in order to use SCTransform-normalised data for LIGER? Do I just start from `RunOptimizeALS`...

Hi, Is it possible for the brackets to be outside the range of the y axis, rather than the axis extending to fit the brackets in? These are percentages, so...

Hi, I am using `stat_cor` and separating the r and p values with "\n". The text ends up centered, however I would like it to be left justified. I tried...

scanorama with reticulate - ERROR: Data sets must be numpy array or scipy.sparse.csr_matrix, received type <class 'str'>.

2

Hi, I am getting an error when following the guidance for running scanorama with reticulate as below: ``` # List of datasets (matrices of cells-by-genes): datasets

BAM filtering query - ok to have multiple primary alignments in BAM file?

7

Hi, In your paper, you say that you "discard those reads with low alignment quality, including MAPQ < 20, aligned length < 30 nt and FLAG with UNMAP, SECONDARY, QCFAIL...

Subsetting donor VCF file for Vireo strategy 2

3

Hi, For strategy 2, you recommend subsetting the donor VCF file as below. Specifically how would you recommend to filter out SNPs with "too much missing values" or "genotypes too...

Vireo taking ages to run

4

Hi, I have some single-cell RNA-seq data for which I don't have genotype information. I ran cellSNP-lite on a merged BAM file containing all of the donors to genotype the...

Clarifying the workflow using bulk RNA-seq data for genotyping

1

Hi, I have bulk RNA-seq data for each of my human samples, plus the scRNA-seq data that I would like to demultiplex with Vireo. Could I just clarify the workflow?...