Resist Portal is a Rshiny portal for the exploration of long read sequencing data generated during the lncrna_resist project. The portal includes modules for explorating Differential Gene Expression (DGE), Differential Transcript Expression (DTE), and Differential Transcript Usage (DTU).
The app is separated in multiple menus:
- Summary: Information on genes/transcripts: positions on the genome, IDs & names, biotype, new (discovered by Bambu) or known (present in the annotation file) genes, filters.
- Count: Read count per transcript for each sample. Counts are normalized based on TPM (transcripts per million).
- DGE: Differential Gene Expression data.
- DTE: Differential Transcript Expression data.
DGE and DTE were performed with DESeq2 per cancer using a negative binomial generalized linear model. Significance of differential gene/transcript expression is defined by p-value adjusted (padj) and log 2 fold change (log2FoldChange). - DTU: Differential Transcript Usage data performed with isoformSwitchAnalyzeR. A significant isoform switch is defined by
alphacorresponding to FDR corrected P-value cut-off anddIFreflecting the effect size.
On every menu, a search bar is here to search a gene (by its name or its gene ID (Ensembl)) get more detail on it. When searching for a gene, a "Query" tab appears to get more specific information on the searched gene.
A ready-to-use version of the application is available on here. It can also be installed from gitHub and launched with the command: runApp('path/to/Resist_Portal'), or with the graphical interface of R studio through the app.R file.
If you choose to install from gitHub, download the following data file in the DATArepository:
DTUall.qs
