Dan Li

Hello: How should I solve this problem? Thanks a lot ```bash snakemake -s ./StainedGlass/workflow/Snakefile --configfile=./StainedGlass/config/config.yaml --config sample=Arabidopsis fasta=./Col-CEN_v1.2.fasta --cores 24 make_figures -p ``` ```bash [INFO] The sequence will be split...

Hello: How should I solve this problem? ```bash snakemake -s ./StainedGlass/workflow/Snakefile --configfile=./StainedGlass/config/config.yaml --config sample=Arabidopsis fasta=./Col-CEN_v1.2.fasta --cores 24 make_figures -p ``` ```bash IndentationError in file D:\R\plots\StainedGlass\workflow\Snakefile, line 51: expected an indented...

BiocManager::install("ggtree"), Error in get(x, envir = ns, inherits = FALSE) : object 'rect_to_poly' not found

2

Hi: ```{r} BiocManager::install("ggtree") ``` How to solve this error? ```{r} Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21) Installing package(s) 'ggtree' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/ggtree_3.8.2.tar.gz' Content type 'application/gzip' length 360923 bytes...

Hi How can I integrate 2 multiome samples and cluster them together? ```{r} pbmc1 = readRDS("./Multiome1.rds") pbmc1 ``` ```{r} An object of class Seurat 122385 features across 1028 samples within...

Hello: When I run the `CoveragePlot` ```{r} CoveragePlot(pbmc, region = 'Erg', features = 'sct_Erg', assay = 'ATAC', expression.assay = 'SCT', peaks = FALSE) ``` How to solve this error? ```{r}...

Hello: How can I filter the features at least expressed in 10 cells? ```{r} pbmc 2000 & nCount_RNA < 25000 & nCount_RNA > 2000 & percent.mt < 20 ) ```...

Error in g$grobs[[legend]]: no such index at level 2

3

When run the tutorial "https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html" The output figures are all correct but when I tried to save them: ```{r} #Save Plot plotPDF(p1, p2, p3, name = "UMAP-scATAC-scRNA-Combined", addDOC = FALSE)...

`addGeneIntegrationMatrix` Error in slot(object = object, name = "features")[[layer]] <- features: more elements supplied than there are to replace Traceback:

10

When run the tutorial in the document: https://www.archrproject.com/bookdown/cross-platform-linkage-of-scatac-seq-cells-with-scrna-seq-cells.html ```{r} projHeme2

`addGeneExpressionMatrix` Error: invalid subscript

1

Hello How can I `addGeneExpressionMatrix` using a `SingleCellAssay` object? I created the `SingleCellAssay` object by: ```{r} seRNA

`createArrowFiles` can't generate "QualityControl" plots

2

I run the codes in the documents: https://www.archrproject.com/bookdown/per-cell-quality-control.html ```{r} ArrowFiles