A survey of best practices for RNA-seq data analysis
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology
Significant innovations in next-generation sequencing techniques and bioinformatics tools
have impacted our appreciation and understanding of RNA. Practical RNA sequencing …
have impacted our appreciation and understanding of RNA. Practical RNA sequencing …
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems
R Liu, AE Loraine, JA Dickerson - BMC bioinformatics, 2014 - Springer
Abstract Background Alternative Splicing (AS) as a post-transcription regulation mechanism
is an important application of RNA-seq studies in eukaryotes. A number of software and …
is an important application of RNA-seq studies in eukaryotes. A number of software and …
ASCOT identifies key regulators of neuronal subtype-specific splicing
Public archives of next-generation sequencing data are growing exponentially, but the
difficulty of marshaling this data has led to its underutilization by scientists. Here, we present …
difficulty of marshaling this data has led to its underutilization by scientists. Here, we present …
Opportunities and methods for studying alternative splicing in cancer with RNA-Seq
The biogenesis, development and metastases of cancer are associated with many variations
in the transcriptome. Alternative splicing of genes is a major post-transcriptional regulation …
in the transcriptome. Alternative splicing of genes is a major post-transcriptional regulation …
Methods to study splicing from high-throughput RNA sequencing data
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq)
has provided a very powerful mean to study splicing under multiple conditions at …
has provided a very powerful mean to study splicing under multiple conditions at …
Metformin Promotes Differentiation and Attenuates H2O2-Induced Oxidative Damage of Osteoblasts via the PI3K/AKT/Nrf2/HO-1 Pathway
K Yang, F Cao, S Qiu, W Jiang, L Tao… - Frontiers in …, 2022 - frontiersin.org
At present, the drug treatment of osteoporosis is mostly focused on inhibiting
osteoclastogenesis, which has relatively poor effects. Metformin is a drug that can potentially …
osteoclastogenesis, which has relatively poor effects. Metformin is a drug that can potentially …
A survey of software for genome-wide discovery of differential splicing in RNA-Seq data
JE Hooper - Human genomics, 2014 - Springer
Alternative splicing is a major contributor to cellular diversity. Therefore the identification and
quantification of differentially spliced transcripts in genome-wide transcript analysis is an …
quantification of differentially spliced transcripts in genome-wide transcript analysis is an …
Differential expression analysis of RNA-seq data at single-base resolution
Abstract RNA-sequencing (RNA-seq) is a flexible technology for measuring genome-wide
expression that is rapidly replacing microarrays as costs become comparable. Current …
expression that is rapidly replacing microarrays as costs become comparable. Current …
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing
SeqGSEA is an open-source Bioconductor package for the functional integration of
differential expression and splicing analysis in RNA-Seq data. SeqGSEA implements an …
differential expression and splicing analysis in RNA-Seq data. SeqGSEA implements an …