Hi Federico, thanks for your app which can really make my work a lot easier!
For the first time I am approaching RNAseq data analysis and I am adapting my data to the documentation workflow. Once I get to the re_enrich part, when I create bg_ids it returns me a NULL value. How can I solve this problem?
I tried adding the annotation to the dds object but I get no results. I'll write to you below my code.

colData <- read.table('DATI_GeneTonic/samples_table.txt', sep='\t', row.names = 1,header = T)
files <- file.path('DATI_GeneTonic', colData$seqname_quant, "quant.sf")
names(files) <- rownames(colData)
tx2gene <- readRDS("DATI_GeneTonic/tx2gene.gencode.v38.annotation.RDS")
head(tx2gene)

txi <- tximport(files, type="salmon", tx2gene=tx2gene)
ddsTxi <- DESeqDataSetFromTximport(txi,
colData = colData,
design = ~kit+condition)
dds <- ddsTxi
dds$symbol <- mapIds(org.Hs.eg.db,
keys=gene_ids,
column="SYMBOL",
keytype="ENSEMBL")
rownames(dds) <- substr(rownames(dds), 1, 15)
keep <- rowSums(counts(dds)) > 0
dds <- dds[keep,]
dds <- DESeq(dds)
res_control_mutant <- results(dds, contrast = c("condition", "control", "mutant"), lfcThreshold = 1, alpha = 0.05)
res_control_mutant$symbol <- mapIds(org.Hs.eg.db,
keys=ens.str,
column="SYMBOL",
keytype="ENSEMBL",
multiVals="first")
de_symbols_control_mutant <- deseqresult2df(res_control_mutant, FDR = 0.05)$symbol

bg_ids <- rowData(dds)$symbol[rowSums(counts(dds)) > 0]
NULL

Thanks
Marco