FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
Motivation: In eukaryotic cells, alternative splicing expands the diversity of RNA transcripts
and plays an important role in tissue-specific differentiation, and can be misregulated in …
and plays an important role in tissue-specific differentiation, and can be misregulated in …
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq
The RNA transcriptome varies in response to cellular differentiation as well as
environmental factors, and can be characterized by the diversity and abundance of transcript …
environmental factors, and can be characterized by the diversity and abundance of transcript …
Identifying differentially spliced genes from two groups of RNA-seq samples
Recent study revealed that most human genes have alternative splicing and can produce
multiple isoforms of transcripts. Differences in the relative abundance of the isoforms of a …
multiple isoforms of transcripts. Differences in the relative abundance of the isoforms of a …
[HTML][HTML] KIS SPLICE: de-novo calling alternative splicing events from RNA-seq data
GAT Sacomoto, J Kielbassa, R Chikhi, R Uricaru… - BMC …, 2012 - Springer
Background In this paper, we address the problem of identifying and quantifying
polymorphisms in RNA-seq data when no reference genome is available, without …
polymorphisms in RNA-seq data when no reference genome is available, without …
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
LH LeGault, CN Dewey - Bioinformatics, 2013 - academic.oup.com
Motivation: Alternative splicing and other processes that allow for different transcripts to be
derived from the same gene are significant forces in the eukaryotic cell. RNA-Seq is a …
derived from the same gene are significant forces in the eukaryotic cell. RNA-Seq is a …
[HTML][HTML] rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test
High-throughput sequencing of transcriptomes (RNA-Seq) has recently become a powerful
tool for the study of gene expression. We present rSeqDiff, an efficient algorithm for the …
tool for the study of gene expression. We present rSeqDiff, an efficient algorithm for the …
rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data
High-throughput sequencing of transcriptomes (RNA-Seq) has become a powerful tool to
study gene expression. Here we present an R package, rSeqNP, which implements a non …
study gene expression. Here we present an R package, rSeqNP, which implements a non …
[HTML][HTML] Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
The emergence of single-cell RNA-seq (scRNA-seq) technology has made it possible to
measure gene expression variations at cellular level. This breakthrough enables the …
measure gene expression variations at cellular level. This breakthrough enables the …
A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies
Over the last few years, RNA-seq has been used to study alterations in alternative splicing
related to several diseases. Bioinformatics workflows used to perform these studies can be …
related to several diseases. Bioinformatics workflows used to perform these studies can be …
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
SS Norton, J Vaquero-Garcia, NF Lahens… - …, 2018 - academic.oup.com
Motivation A key component in many RNA-Seq-based studies is contrasting multiple
replicates from different experimental conditions. In this setup, replicates play a key role as …
replicates from different experimental conditions. In this setup, replicates play a key role as …