This document shows how to use XAEM [Deng et al., 2019] to quantify isoform expression for multiple samples. What are new in version 0.1.2. Improve speed and fix bug for building CRP to work with complex annotations such as GENCODE and ENSEMBL, which usually have >200,000 isoforms for hg38.

This section presents a tutorial to run XAEM pipeline with a toy example. Suppose that input data contain two RNA-seq samples and server supplies 4 CPUs for computation. We can test XAEM by just copy and paste of the example commands. Download the binary file of XAEM

Aug 10, 2019 · We use an alternating expectation-maximization (AEM) algorithm, alternating between estimation of X and β. For speed XAEM utilizes quasi-mapping for read alignment, thus leading to a fast algorithm. Overall XAEM performs favorably compared to recent advanced methods. For simulated datasets, XAEM obtains higher accuracy for multiple-isoform genes.

This document shows how to use XAEM [Deng et al., 2019] to quantify isoform expression for multiple samples. Software requirements for XAEM: Annotation reference: XAEM requires a fasta file of transcript sequences and a gtf file of transcript annotation. XAEM supports all kinds of reference and annotation for any species.

Feb 1, 2020 · Compared to existing methods, XAEM automatically performs empirical correction of potentially unknown biases. We use an alternating expectation-maximization (AEM) algorithm, alternating between estimation of X and β.

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XAEM for quantification of isoform expression. Contribute to WenjiangDeng/XAEM development by creating an account on GitHub.

Annotation reference: XAEM requires a fasta file of transcript sequences and a gtf file of transcript annotation. XAEM supports all kinds of reference and annotation for any species. In the XAEM paper, we use the UCSC hg19 annotation: 2. Download and installation. If you use the binary version of XAEM (recommended):

XAEM is a novel computational method for estimating isoform-level gene expression from RNA-seq data. Unlike existing methods that rely on simplifying assumptions and known biases, XAEM employs a more flexible and robust statistical model called the bilinear model.

Sep 6, 2021 · XAEM implements the design matrix and alternating EM (AEM) algorithm, which allows a fast and accurate quantification of isoform expression using multiple samples. In differential expression (DE) analysis of single-cell data …