L-RAPiT: Long Read Analysis Pipeline for Transcriptomics is an easy-to-use publicly available pipeline which allows for analysis of long read RNA-sequencing data within a cloud environment; namely, Google Colaboratory. L-RAPiT is available at the following address: https://github.com/Theo-Nelson/long-read-sequencing-pipeline Citation: Nelson, T.M.; ...
Read More »AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data
A simplistic understanding of the central dogma falls short in correlating the number of genes in the genome to the number of proteins in the proteome.
Read More »Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq
RNA-seq is a promising approach to improve diagnoses by detecting pathogenic aberrations in RNA splicing that are missed by DNA sequencing...
Read More »Improved barley transcriptome
The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a ...
Read More »Alternative splicing signature analysis unveils prognostic predictor for kidney renal clear cell carcinoma
There is growing evidence that alternative splicing (AS) plays an important role in cancer development. However, a comprehensive analysis of AS signatures in kidney renal clear cell carcinoma (KIRC) is lacking and urgently needed. It remains unclear whether AS acts ...
Read More »Alternative splicing, RNA-seq and drug discovery
Alternative splicing (AS) is an essential component of gene expression regulation that contributes to the diversity of proteomes. Recent developments in RNA sequencing (RNA-seq) technologies, combined...
Read More »ASGAL – aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
While the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events...
Read More »A viable alternative to RNA-seq for detection of alternative splicing events?
RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene...
Read More »Portcullis – efficient and accurate detection of splice junctions from RNA-Seq
Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression and alternative splicing. Key to this is the the accurate identification of...
Read More »SpliceVec – Distributed feature representations for splice junction prediction
Identification of intron boundaries, called splice junctions, is an important part of delineating gene structure and functions. This also provides...
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