This package is still under development, although this version is stable and can be used.
ORFik is a R package containing various functions for analysis of Ribo-Seq, RNA-Seq, CAGE and TCP-seq data related to transcriptomics. ORFik currently supports:
Package is available from bioconductor (3.12, R version >= 4.0.0)
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("ORFik")
Development version on bioconductor (3.13, R version >= 4.0.0)
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("ORFik", version = "devel")
Package is also available here on github
After installation run:
library(ORFik) # Tissue specific 5' utrs using cage-data ?reassignTSSbyCage # Detecting open reading frames ?findORFs # get a feature-set from predicted orfs ?computeFeatures # read vignette browseVignettes("ORFik")
Please feel free to provide feedback or desired functionality by creating a new issue on our github page.
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