tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
L de la Fuente, Á Arzalluz-Luque, M Tardáguila… - Genome biology, 2020 - Springer
Recent advances in long-read sequencing solve inaccuracies in alternative transcript
identification of full-length transcripts in short-read RNA-Seq data, which encourages the …
identification of full-length transcripts in short-read RNA-Seq data, which encourages the …
Towards reliable isoform quantification using RNA-SEQ data
Background In eukaryotes, alternative splicing often generates multiple splice variants from
a single gene. Here weexplore the use of RNA sequencing (RNA-Seq) datasets to address …
a single gene. Here weexplore the use of RNA sequencing (RNA-Seq) datasets to address …
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data
Integrating large-scale functional genomic data has significantly accelerated our
understanding of gene functions. However, no algorithm has been developed to differentiate …
understanding of gene functions. However, no algorithm has been developed to differentiate …
nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
Abstract Motivation Iso-Seq RNA long-read sequencing enables the identification of full-
length transcripts and isoforms, removing the need for complex analysis such as …
length transcripts and isoforms, removing the need for complex analysis such as …
Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data
Genome-wide analyses estimate that more than 90% of multi exonic human genes produce
at least two transcripts through alternative splicing (AS). Various bioinformatics methods are …
at least two transcripts through alternative splicing (AS). Various bioinformatics methods are …
BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments
Y Huang, G Sanguinetti - Genome biology, 2021 - Springer
RNA splicing is an important driver of heterogeneity in single cells through the expression of
alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic …
alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic …
Evaluation and comparison of computational tools for RNA-seq isoform quantification
Background Alternatively spliced transcript isoforms are commonly observed in higher
eukaryotes. The expression levels of these isoforms are key for understanding normal …
eukaryotes. The expression levels of these isoforms are key for understanding normal …
Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing
Background RNA-Seq has become a key technology in transcriptome studies because it can
quantify overall expression levels and the degree of alternative splicing for each gene …
quantify overall expression levels and the degree of alternative splicing for each gene …
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Background RNA-seq data is currently underutilized, in part because it is difficult to predict
the functional impact of alternate transcription events. Recent software improvements in full …
the functional impact of alternate transcription events. Recent software improvements in full …
The emerging era of genomic data integration for analyzing splice isoform function
The vast majority of multi-exon genes in humans undergo alternative splicing, which greatly
increases the functional diversity of protein species. Predicting functions at the isoform level …
increases the functional diversity of protein species. Predicting functions at the isoform level …