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Metagenomic Data Analysis
This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control...
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Development of an optimization pipeline of asymmetric PCR towards the generation of DNA aptamers: a guide for beginners
AbstractAsymmetric PCR is one of the most utilized strategies in ssDNA generation towards DNA aptamer generation due to its low cost, robustness and...
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A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures
BackgroundThe accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific...
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Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline
The continued improvement of combinatorial CRISPR screening platforms necessitates the development of new computational pipelines for scoring...
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A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new insights into proliferative diabetic retinopathy
BackgroundVitreous is an accessible, information-rich biofluid that has recently been studied as a source of retinal disease-related proteins and...
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RNA-Sequencing Analysis Pipeline for Prognostic Marker Identification in Cancer
Sequencing analysis finds many applications in various fields of biology from comparative genomics to clinical research. Recent studies, using...
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The Divider Assay is a high-throughput pipeline for aggression analysis in Drosophila
Aggression is a complex social behavior that remains poorly understood. Drosophila has become a powerful model system to study the underlying biology...
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AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance
We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best...
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
BackgroundPacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have...
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SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs
Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our...
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Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets
BackgroundSingle-cell RNA sequencing (scRNA-seq) has quickly become one of the most dominant techniques in modern transcriptome assessment. In...
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Virtual reality-empowered deep-learning analysis of brain cells
Automated detection of specific cells in three-dimensional datasets such as whole-brain light-sheet image stacks is challenging. Here, we present...
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Data Processing and Germline Variant Calling with the Sentieon Pipeline
Public and private genomic sequencing initiatives generate ever-increasing amounts of genomic data creating a need for improved solutions for...
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A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease
BackgroundCongenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully...
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scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing
BackgroundSingle-cell RNA sequencing is a state-of-the-art technology to understand gene expression in complex tissues. With the growing amount of...
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High-Throughput Protein–Protein Interactions Screening Using Pool-Based Liquid Yeast Two-Hybrid Pipeline
Because of its adaptability to high-throughput approaches and a low operating cost, the yeast two-hybrid (Y2H) assay remains the most widely used one...
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Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC map** pipeline
BackgroundWith high-efficient water-use and drought tolerance, broomcorn millet has emerged as a candidate for food security. To promote its research...
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Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the...
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Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction
BackgroundRNA velocity is a novel and powerful concept which enables the inference of dynamical cell state changes from seemingly static single-cell...
