diff --git a/Deseq2/Deseq2.r b/Deseq2/Deseq2.r
deleted file mode 100644
index 17923b4..0000000
--- a/Deseq2/Deseq2.r
+++ /dev/null
@@ -1,157 +0,0 @@
-# March 10, 2023
-
-suppressWarnings(library('optparse'))
-
-script.desc <-
-'Calculates differential expression using DESeq2.
-User must supply the RDS of a Seurat object (-r) which must contain cell identities annotated by SingleR.
-User must also supply a scReadCounts output file (-t) which contains the SNV
-position and number of reads.
-User can supply cell type (-c) or a short list of SNVs (-l) to analyze.'
-
-parser <- OptionParser(description=script.desc)
-parser <- add_option(parser, c('-r', '--rds-file'),
-                     type='character',
-                     help='RDS file containing Seurat object.')
-parser <- add_option(parser, c('-t', '--snv-file'),
-                     type='character',
-                     help='File containg SNVs.')
-parser <- add_option(parser, c('-c', '--cell-types'),
-                     type='character',
-                     help='List of cell types to analyze.')
-parser <- add_option(parser, c('-l', '--short-list'),
-                     type='character',
-                     help='File containg short list of SNVs.')
-parser <- add_option(parser, c('-x', '--use-sctype'),
-                     type='logical', default=F, action='store_true',
-                     help='Use scType instead of SingleR.')
-args <- parse_args(parser)
-
-error.msg <- NULL
-
-# Check if the required argument (-r) is passed
-if (is.null(args$`rds-file`))
-  error.msg <- paste(error.msg, '- Seurat RDS object (-r) is required.',
-                     sep='\n')
-if (is.null(args$`snv-file`))
-  error.msg <- paste(error.msg, '- SNV data (-t) is required.',
-                     sep='\n')
-
-# Check if there are any errors
-if (!is.null(error.msg)) {
-  print_help(parser)
-  stop(error.msg)
-}
-
-
-######
-# Application Logic
-######
-
-library('Seurat')
-library('EnhancedVolcano')
-library('DESeq2')
-srt <- readRDS(args$`rds-file`)
-snv.data <- read.table(args$`snv-file`, sep='\t', header=T)
-
-if (args$`use-sctype`) { # Hack to make it compatiable with scType
-  srt[['SingleR.cluster.labels']] <- srt[['customclassif']]
-}
-
-calculateDEx <- function(srt, snv.sub, cell.type) {
-  # Check if SNV list only has one SNV position
-  stopifnot(nrow(unique(snv.sub[, 1:4]))==1)
-  
-  # Find cell types
-  bc <- srt[['SingleR.cluster.labels']]
-
-  # Differentiate cell types
-  bc[bc$SingleR.cluster.labels!=cell.type, 'SNV'] <- 'Irrelevant'
-  bc[bc$SingleR.cluster.labels==cell.type, 'SNV'] <- 'Undetected'
-
-  # Find barcodes that contain 0 and non-0 VAF
-  bc.ref <- snv.sub$ReadGroup[snv.sub$VAF==0]
-  bc.ref <- bc.ref[!is.na(bc.ref)]
-  bc.alt <- snv.sub$ReadGroup[snv.sub$VAF>0]
-  bc.alt <- bc.alt[!is.na(bc.alt)]
-
-  # Set reference or alternate
-  bc[(rownames(bc) %in% bc.ref) & (bc$SNV=='Undetected'), 'SNV'] <- 'Ref'
-  bc[(rownames(bc) %in% bc.alt) & (bc$SNV=='Undetected'), 'SNV'] <- 'Alt'
-
-  srt.snv <- srt
-  stopifnot(rownames(bc)==colnames(srt.snv))
-
-  # Assign SNV information to Seurat meta-data
-  srt.snv[['SNV']] <- bc$SNV
-  
-  if (sum(srt.snv[['SingleR.cluster.labels']]==cell.type) == 0)
-    stop('Cell type not found in dataset.')
-  if (sum(srt.snv[['SNV']]=='Alt') < 3 || sum(srt.snv[['SNV']]=='Ref') < 3)
-    stop('Not enough Ref/Alt reads for analysis.')
-  suppressMessages(
-    res.dex <- FindMarkers(srt.snv, ident.1='Alt', ident.2='Ref',
-                           group.by='SNV', test.use='DESeq2', assay='RNA')
-  )
-  res.dex <- res.dex[order(res.dex$p_val_adj, res.dex$p_val), ]
-
-  # Print out status msg before returning value
-  message(paste0('\nSNV: ', snv.sub[1, 1], ':', snv.sub[1, 2], ' ',
-                            snv.sub[1, 3], '>', snv.sub[1, 4], '\n',
-                 'Cell type: ', cell.type), '\n',
-                 'With Ref: ', sum(bc$SNV=='Ref'), '; ',
-                 'With SNV: ', sum(bc$SNV=='Alt'))
-  res.dex
-}
-
-
-snv.list <- unique(snv.data[, 1:4])
-if (!is.null(args$`cell-types`)) {
-  cell.types <- unlist(strsplit(gsub('[\'\"]', '', args$`cell-types`), ','))
-} else {
-  cell.types <- unique(srt[['SingleR.cluster.labels']][, 1])
-}
-message(paste0('Analyzing: ', paste(unlist(cell.types), collapse=', ')))
-
-# Reduce the list
-if (!is.null(args$`short-list`)) {
-  snv.short <- read.table(args$`short-list`, sep='\t', header=T,
-                          colClasses=c('character', 'character', 'character',
-                          'character')) 
-  snv.list <- merge(snv.list, snv.short, by=c('CHROM', 'POS', 'REF', 'ALT'))
-  snv.list <- unique(snv.list)
-}
-
-
-suppressWarnings(dir.create('output'))
-for (i in 1:nrow(snv.list)) {
-  for (cell.type in cell.types) {
-    # Put together name
-    data.name <- substr(gsub(' ', '', cell.type), 1, 5)
-    data.name <- paste0(data.name, '_',
-                        snv.list$CHROM[i], '_',
-                        snv.list$POS[i], '_', 
-                        snv.list$REF[i], '_', 
-                        snv.list$ALT[i])
-
-    snv.sub <- subset(snv.data, CHROM==snv.list$CHROM[i] &
-                                POS==snv.list$POS[i] &
-                                REF==snv.list$REF[i] &
-                                ALT==snv.list$ALT[i])
-    tryCatch({
-      res <- calculateDEx(srt, snv.sub, cell.type)
-      write.table(res, paste0('output/DE_', data.name, '.txt'),
-                  sep='\t', col.names=NA)
-      suppressMessages({
-        EnhancedVolcano(res, lab=rownames(res), x='avg_log2FC', y='p_val',
-                        title=paste0(snv.sub[1, 1], ':', snv.sub[1, 2], ' ',
-                              snv.sub[1, 3], '>', snv.sub[1, 4]),
-                        subtitle=NULL, pCutoff=0.05)
-        ggsave(paste0('output/DE_', data.name, '_volc.png'))
-      })
-      },
-      error=function (e) {
-        warning(paste0('Issue with ', data.name, '.\n'), e$message)}
-    )
-  }
-}