Cargando…

DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization

RNA-seq analysis of alternative pre-mRNA splicing has facilitated an unprecedented understanding of transcriptome complexity in health and disease. However, despite the availability of countless bioinformatic pipelines for transcriptome-wide splicing analysis, the use of these tools is often limited...

Descripción completa

Detalles Bibliográficos
Autores principales:	Gallego-Paez, Lina Marcela, Mauer, Jan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2022
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580925/ https://www.ncbi.nlm.nih.gov/pubmed/36304260 http://dx.doi.org/10.3389/fbinf.2022.786898

Ejemplares similares

Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome
por: Slabaugh, Erin, et al.
Publicado: (2019)

Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data
por: Kroll, Jose E., et al.
Publicado: (2015)

Splicing predictions reliably classify different types of alternative splicing
por: Busch, Anke, et al.
Publicado: (2015)

Uncertainty Visualization: Concepts, Methods, and Applications in Biological Data Visualization
por: Weiskopf, Daniel
Publicado: (2022)

BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser
por: Raveendran, Karthik, et al.
Publicado: (2022)

Visualization of RNA structure models within the Integrative Genomics Viewer
por: Busan, Steven, et al.
Publicado: (2017)

Exploring the Microbiome Analysis and Visualization Landscape
por: Peeters, Jannes, et al.
Publicado: (2021)

Integrated analysis of the roles and prognostic value of RNA binding proteins in lung adenocarcinoma
por: Li, Wei, et al.
Publicado: (2020)

Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR
por: Estrada, April D., et al.
Publicado: (2015)

Splicing conservation signals in plant long noncoding RNAs
por: Corona-Gomez, Jose Antonio, et al.
Publicado: (2020)

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi
por: Zafrir, Zohar, et al.
Publicado: (2015)

Identification of crucial aberrantly methylated and differentially expressed genes related to cervical cancer using an integrated bioinformatics analysis
por: Ma, Xiaoling, et al.
Publicado: (2020)

Leveraging transcript quantification for fast computation of alternative splicing profiles
por: Alamancos, Gael P., et al.
Publicado: (2015)

RBP-Maps enables robust generation of splicing regulatory maps
por: Yee, Brian A., et al.
Publicado: (2019)

Predicting the effect of variants on splicing using Convolutional Neural Networks
por: Thanapattheerakul, Thanyathorn, et al.
Publicado: (2020)

Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing
por: Radens, Caleb M., et al.
Publicado: (2020)

Identification of prognostic and metastasis-related alternative splicing signatures in hepatocellular carcinoma
por: Huang, Runzhi, et al.
Publicado: (2020)

Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: Application to cell division and morphogenesis analysis
por: Fouché, Gwendal, et al.
Publicado: (2023)

CPJSdraw: analysis and visualization of junction sites of chloroplast genomes
por: Li, Huie, et al.
Publicado: (2023)

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
por: Nitsche, Anne, et al.
Publicado: (2015)

Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses
por: Ding, Yiqian, et al.
Publicado: (2020)

Identification of prognostic splicing factors and exploration of their potential regulatory mechanisms in pancreatic adenocarcinoma
por: Rong, Min-hua, et al.
Publicado: (2020)

Integrated analysis of differentially expressed profiles and construction of a competing endogenous long non-coding RNA network in renal cell carcinoma
por: Xing, Qianwei, et al.
Publicado: (2018)

Anvi’o: an advanced analysis and visualization platform for ‘omics data
por: Eren, A. Murat, et al.
Publicado: (2015)

fluff: exploratory analysis and visualization of high-throughput sequencing data
por: Georgiou, Georgios, et al.
Publicado: (2016)

EPIphany—A Platform for Analysis and Visualization of Peptide Immunoarray Data
por: Parker Cates, Zoe, et al.
Publicado: (2021)

clipplotr—a comparative visualization and analysis tool for CLIP data
por: Chakrabarti, Anob M., et al.
Publicado: (2023)

A sequence-based, deep learning model accurately predicts RNA splicing branchpoints
por: Paggi, Joseph M., et al.
Publicado: (2018)

Genome-wide identification, evolution, expression, and alternative splicing profiles of peroxiredoxin genes in cotton
por: Feng, Yulong, et al.
Publicado: (2021)

IsoSplitter: identification and characterization of alternative splicing sites without a reference genome
por: Wang, Yupeng, et al.
Publicado: (2021)

ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences
por: Ejigu, Girum Fitihamlak, et al.
Publicado: (2021)

DDX17 modulates the expression and alternative splicing of genes involved in apoptosis and proliferation in lung adenocarcinoma cells
por: He, Cheng, et al.
Publicado: (2022)

Comprehensive characterization of the alternative splicing landscape in ovarian cancer reveals novel events associated with tumor-immune microenvironment
por: Sun, Dan, et al.
Publicado: (2022)

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci
por: Haerty, Wilfried, et al.
Publicado: (2015)

Biological classification with RNA-seq data: Can alternatively spliced transcript expression enhance machine learning classifiers?
por: Johnson, Nathan T., et al.
Publicado: (2018)

Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas
por: Yang, Lingpeng, et al.
Publicado: (2019)

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
por: Delmont, Tom O., et al.
Publicado: (2016)

intansv: an R package for integrative analysis of structural variations
por: Jia, Lihua, et al.
Publicado: (2020)

Integrated Cells and Collagen Fibers Spatial Image Analysis
por: Vasiukov, Georgii, et al.
Publicado: (2021)

GOLPH3 modulates expression and alternative splicing of transcription factors associated with endometrial decidualization in human endometrial stromal cells
por: Zhu, Suqin, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_8pgnbrduuro8i3emf5vhg70lrb