Welcome to this R shiny app!

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Update (2024 Jan 31)

Bioconductor package STAN local installation is avaliable with 'STAN.zip' (genoSTAN 2.24.0):

install.packages("YOUR_PATH/STAN", repo = NULL, type = "source")

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Transcription unit (TU) annotation tool for nascent RNA-Seq analysis.

Usage:

• transcribed genomic regions (e.g. non-coding intergenic RNAs)
• multiple transcriptomes comparison (e.g. GRO-seq vs PRO-seq)
• alternative to HOMER's GRO-seq analysis, with an optional mRNA TU merging step (recommended).

Inputs:

1. gene reference (GENCODE or ensembl)
2. bam files (allow multiple files from replicates)

Output:

• gff3 files of TU intervals (in a zipped folder)
  • with columns: expression, gene id, transript id, exon overlap, gene type, relative location to gene.

Non-coding TUs will be named according to their relative locations to the neighbored genes.

Scattered TU intervals overlapping with gene references will be joined with a selected method:

• by TU (3' termination region will often be included)
• by exon (only keeps TU intervals within gene boundary, for accurate expression level estimation, but also produces trimmed flanking TUs)