whitneyt

Hello! When plotting the DE genes found with DEG() for multiple subtypes, I receive the following error `>res_cat

Failed to install 'iTALK'...unable to access index for respo

6

Hello, I get the error below: ``` Error: Failed to install 'iTALK' from GitHub: (converted from warning) unable to access index for repository https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5: cannot open URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/PACKAGES' ``` I...

Error: `order` should contain names of all sectors. when running LRPlot with DEG datatype

2

Hello, I am trying to run differential expression between Tumor and Tcells LR pairs but am getting `Error: order should contain names of all sectors` ![Screen Shot 2020-05-06 at 5...

Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

1

Hello! I am trying to run DEG function with method="DESeq2" between three groups for single cell RNA seq data. `deg_BcellsM% filter(cell_type=='B-cells-M'),method='DESeq2',contrast=c("grouped_pd","grouped_pr","naive")) ` but am getting the following output: `Found more...

I have a large object with 36 visium reactions that I have SCTransformed -> rpca integrated -> performed downstream analysis. I would now like to sub-cluster the larger clusters by...

Hello! After adjusting the n_cut=k k value, how do we save the new files in all of the appropriate respective files? I understand to how to save them individually, but...

Option to aggregate individual MistyData objects from multiple samples

4

Hello! Thank you for this package. I'm looking to run this pipeline on 36 Visium reactions and mistyR has the option to run MISTy on multiple individual samples and aggregate...

Using MISTy on multiple samples

2

Hello, I'm interested in applying MISTy to 36 visium reactions across four timepoints. Do you have recommendations on how to implement MISTy to help identify spatially relevant features that may...

other parameters to adjust when [1] "No CNV remains after filtering by LLR in pseudobulks. Consider reducing min_LLR."?

1

Hello! I am running numbat on 36 lung tumor cryo visium reactions. My normal reference is a at tumor-adjacent "normal" visium reaction that has been confirmed to be tumor-free by...