Systematic identification and characterization of viral small RNAs from small RNA‐Seq data
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Medical Virology"
DOI: 10.1002/jmv.28617
Abstract: Virus‐encoded small RNAs (vsRNAs) have been reported to play an important role in viral infections. Unfortunately, there is still a lack of a systematic characterization and resource of vsRNAs. Herein, we identified a total of… read more here.
Keywords: seq data; vsrnas identified; rna seq; small rna ... See more keywords
RNA-Seq Data Analysis in Galaxy.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1307-8_20
Abstract: A complete RNA-Seq analysis involves the use of several different tools, with substantial software and computational requirements. The Galaxy platform simplifies the execution of such bioinformatics analyses by embedding the needed tools in its web… read more here.
Keywords: data analysis; analysis; seq data; analysis galaxy ... See more keywords
RAP: A Web Tool for RNA-Seq Data Analysis.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1307-8_21
Abstract: Since 1950 main studies of RNA regarded its role in the protein synthesis. Later insights showed that only a small portion of RNA codes for proteins where the rest could have different functional roles. With… read more here.
Keywords: web tool; analysis; rna seq; seq data ... See more keywords
RNA-Seq Data Analysis: From Raw Data Quality Control to Differential Expression Analysis.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7286-9_23
Abstract: As a revolutionary technology for life sciences, RNA-seq has many applications and the computation pipeline has also many variations. Here, we describe a protocol to perform RNA-seq data analysis where the aim is to identify… read more here.
Keywords: analysis; rna seq; data analysis; seq data ... See more keywords
iSeq: Web-Based RNA-seq Data Analysis and Visualization.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7717-8_10
Abstract: Transcriptome sequencing (RNA-seq) is becoming a standard experimental methodology for genome-wide characterization and quantification of transcripts at single base-pair resolution. However, downstream analysis of massive amount of sequencing data can be prohibitively technical for wet-lab… read more here.
Keywords: seq; data analysis; seq data; iseq ... See more keywords
RNA Pol II transcription model and interpretation of GRO-seq data
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Mathematical Biology"
DOI: 10.1007/s00285-016-1014-4
Abstract: A mixture model and statistical method is proposed to interpret the distribution of reads from a nascent transcriptional assay, such as global run-on sequencing (GRO-seq) data. The model is annotation agnostic and leverages on current… read more here.
Keywords: rna pol; model; gro seq; seq data ... See more keywords
The priming fingerprint on the plant transcriptome investigated through meta-analysis of RNA-Seq data
Sign Up to like & getrecommendations! Published in 2020 at "European Journal of Plant Pathology"
DOI: 10.1007/s10658-019-01928-3
Abstract: Plants may enter into a state of alert that allows them to deploy defensive measures in a more effective way upon stress occurrence. This phenomenon is termed defense priming, and it is started in plants… read more here.
Keywords: plant; seq data; transcriptome; rna seq ... See more keywords
Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv.
Sign Up to like & getrecommendations! Published in 2020 at "Cell systems"
DOI: 10.1016/j.cels.2020.02.009
Abstract: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility due to its time and input material efficiency. However, it can be difficult to evaluate data quality and identify… read more here.
Keywords: atac seq; seq data; bias; bias atac ... See more keywords
A semi-supervised deep learning method based on stacked sparse auto-encoder for cancer prediction using RNA-seq data
Sign Up to like & getrecommendations! Published in 2018 at "Computer methods and programs in biomedicine"
DOI: 10.1016/j.cmpb.2018.10.004
Abstract: BACKGROUND AND OBJECTIVE Cancer has become a complex health problem due to its high mortality. Over the past few decades, with the rapid development of the high-throughput sequencing technology and the application of various machine… read more here.
Keywords: semi supervised; supervised deep; seq data; cancer ... See more keywords
ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering
Sign Up to like & getrecommendations! Published in 2021 at "Computational biology and chemistry"
DOI: 10.1016/j.compbiolchem.2020.107415
Abstract: Accurate clustering of cells from single-cell RNA sequencing (scRNA-seq) data is an essential step for biological analysis such as putative cell type identification. However, scRNA-seq data has high dimension and high sparsity, which makes traditional… read more here.
Keywords: seq; similarity; scgslc; seq data ... See more keywords
A road map for happiness: The psychological factors related cell types in various parts of human body from single cell RNA-seq data analysis
Sign Up to like & getrecommendations! Published in 2022 at "Computers in biology and medicine"
DOI: 10.1016/j.compbiomed.2022.105286
Abstract: Massive evidence from all sources including zoology, neurobiology and immunology has confirmed that psychological factors can raise remarkable physiological effects. Researchers have long been aware of the potential value of these effects and wanted to… read more here.
Keywords: single cell; seq data; psychological factors; cell ... See more keywords