The elaborate method for quantification of allele-specific expression on poly-A RNA-seq data.
This R-package performs sample overdispersion estimation from RNA spike-ins or technical replication.
Paper: Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale, A. Mendelevich, S. Gupta, A. Pakharev, A. Teodosiadis, A. A. Mironov, A. A. Gimelbrant
remotes::install_github("gimelbrantlab/controlFreq")
compute_iQCC_for_selected_samples(df = allelic-counts-table, reps = 1:10, sup_Q = 30)
see Wiki for more details.
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For allelic bias test and differential AI test, see Qllelic R-package functions and "Replicate sequencing libraries are important for quantification of allelic imbalance", A.Mendelevich et.al.
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For data preprocessing procedure used in the paper and relevant recommendations, see fastq2allelictabs repository.
Figure above was made in biorender.