allele-specific-expression

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

Mixture Models for Allelic Imbalance Estimation

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq

early version of (Pipeline for detection of differential allelic imbalance from RNA-seq)

C++ Implementation of EMASE

Allele-specific analysis of RNA-seq and DNA-seq data

Integrated Mapping and Profiling of Allelically-expressed Loci with Annotations

aScan is a software tool for the determination of allele-specific-expression at the single individual level from matched RNA-Seq and genomic data.

HLAXPress performs estimation of allele-specific expression levels for HLA genes using UMIs.

Replicating the bioinformatics and statistics pipelines for allele-specific expression analysis of ovary tissue from sterile and reproductive reciprocally crossed honey bees as described in Galbraith et al. (2016). PNAS. https://www.pnas.org/content/113/4/1020

An R package to perform Spatial dissimilarity analysis in single cells

A computational framework to quantify individual-level NMD efficiency and assess its variability across human tissues, tumors and individuals using RNA-seq and WES data

Allele-specific expression (ASE) for short tandem repeats (STRs)

Allele-specific expression analysis detecting genes where one parental copy is preferentially expressed.

This tutorial demonstrates best practices for processing whole genome sequence (WGS) and mRNA sequencing (mRNA-seq) reads for allele-specific transcriptomics analysis.

Beyond conflict: intragenomic conflict predicts individual variation in altruistic behaviour.

Early-stage R tools for covariate-aware allele-specific expression with beta-binomial mixed models, diagnostics and coefficient shrinkage.

A package for analyzing allele-specific expression in polyploid organisms

Network-based stratification of allele-specific expression reveals patient subgroups in Huntington’s disease

High-performance fungal genome annotation pipeline — from raw assembly through NCBI submission, plus integrated RNA-seq stack with allele-specific expression. 24 commands, 15 annotation sources, 25 NCBI genetic codes, JSON reproducibility manifests. Written in Rust.