daskelly

wilcox_unequal_var <- function(x, y, ...) {
  # The Wilcoxon rank sum test (Mann Whitney U test) does not perform
  # that well on data where the variances are unequal. Some
  # investigators have recommended as an alternative performing the
  # unequal variance t-test on ranked values. See
  # https://academic.oup.com/beheco/article/17/4/688/215960
  # https://psycnet.apa.org/doiLanding?doi=10.1037%2Fh0078850
  rr <- rank(c(x, y))
  nx <- length(x)
  t.test(rr[1:nx], rr[(nx+1):length(rr)], var.equal=FALSE, ...)

daskelly

# List all open tabs in front Chrome window
# From https://superuser.com/questions/276321/how-to-export-opened-tabs-in-chrome
alias listtabs="osascript -e{'set o to\"\"','tell app\"google chrome\"','repeat with t in tabs of window 1','set o to o&url of t&\" \"&title of\
 t&linefeed',end,end}|sed \$d"

daskelly

library(ensembldb)
library(EnsDb.Mmusculus.v79)
ensembl_gene_ids <- c('ENSMUSG00000000120', 'ENSMUSG00000000159', 'ENSMUSG00000000563', 'ENSMUSG00000000600')  # some random IDs
ensembldb::select(EnsDb.Mmusculus.v79, keys=ensembl_gene_ids, keytype = "GENEID", columns = c("SYMBOL","GENEID"))

daskelly

library(DT)
#
# make a table of results
# ...
#
datatable(signif_results, filter = 'top', rownames = FALSE,
    options=list(pageLength = 10, autoWidth = TRUE))

daskelly

library(Seurat)
library(harmony)

# x is a Seurat object not yet processed but we have chosen num_pc
x <- FindNeighbors(x, reduction = 'pca', dims = 1:num_pc, verbose = FALSE) %>%
  FindClusters(verbose = FALSE, resolution = 0.2) %>%
  RunUMAP(reduction = 'pca', dims = 1:num_pc, verbose = FALSE)
x$noharmony_clusters <- x$seurat_clusters
x@misc$noharmony_umap <- x@reductions$umap