I downloaded the newest version of R as I kept getting prompted to update in RStudio. As I did, for some reason, previous work I had done following the DESeq2 vignette would not run properly giving me many errors like: 'DESeq2' package doesn't exist. I'll show my most recent errors but I can't run DESeq2 at all.

Code should be placed in three backticks as shown below

library("DESeq2")
install.packages("DESeq2")

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")

#cts1 is female treated v. control on control diet

cts1 <- read.csv("*path to files*/cts1.csv",row.names='gene_id')
coldata1 <- read.csv("*path to files*/Table1.csv", row.names=1)

dds1 <- estimateSizeFactors(dds)
idx <- rowSums( counts(dds, normalized=TRUE) >= 5 ) >= 3


#error I receive
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'estimateSizeFactors': object 'dds' not found

object 'dds' not found

Please learn to read the error message. It's not a DESeq2 problem, dds simply is not defined as variable. You need to construct it via DESeqDataSetFromMatrix() or similar functions. Also, install.packages("DESeq2") won't do as it is a Bioconductor and not a CRAN package. BiocManager::install("DESeq2") is correct, but after install you still need library(DESeq2).