A comparison of statistical methods for detecting differentially expressed genes from RNA‐seq data

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Items 101–200 of 286

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2. Comparative studies of differential gene calling using RNA-Seq data
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3. Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes
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5. Variation in the Transcriptome Response and Detoxification Gene Diversity Drives Pesticide Tolerance in Fishes
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6. Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis
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7. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis
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8. Bioinformatics for RNA‐Seq Data Analysis
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9. Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference
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10. A skellam model to identify differential patterns of gene expression induced by environmental signals
    Libo Jiang, Ke Mao, Rongling Wu · 2014 · BMC Genomics
11. Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species
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12. Exogenous melatonin enhances cell wall response to salt stress in common bean (Phaseolus vulgaris) and the development of the associated predictive molecular markers
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13. Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a “Three-Sample” Scenario
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14. hmmSeq: A hidden Markov model for detecting differentially expressed genes from RNA-seq data
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15. A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses
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16. TrACES of time: Transcriptomic analyses for the contextualization of evidential stains – Identification of RNA markers for estimating time-of-day of bloodstain deposition
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17. Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges
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18. NGS-Trex: Next Generation Sequencing Transcriptome profile explorer
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19. Identifying Breast Cancer-induced Gene Perturbations and its Application in Guiding Drug Repurposing
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20. 2-Deoxy-D-glucose Alleviates Collagen-Induced Arthritis of Rats and Is Accompanied by Metabolic Regulation of the Spleen and Liver
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21. Next-Generation Sequencing Applied to Flower Development: RNA-Seq
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22. Transcriptome analysis during fruit developmental stages in durian (Durio zibethinus Murr.) var. D24
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23. RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants
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24. Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data
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25. Whole-Transcriptome Sequencing for High-Resolution Transcriptomic Analysis in Mycobacterium tuberculosis
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26. An automated RNA‐Seq analysis pipeline to identify and visualize differentially expressed genes and pathways in CHO cells
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27. From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
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28. Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
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29. Transcriptomic analysis revealed potential regulatory biomarkers and repurposable drugs for breast cancer treatment
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30. A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
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31. Transcriptome software results show significant variation among different commercial pipelines
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32. High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report
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33. Using RNA-seq Data to Detect Differentially Expressed Genes
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34. Development of Reference Genes for Horticultural Plants
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35. Differential expression analysis for sequence count data via mixtures of negative binomials
    Elisabetta Bonafede · 2015 · AMS Dottorato Institutional Doctoral Theses Repository (University of Bologna)
36. Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera
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37. Transcriptomic impacts and potential routes of detoxification in a lampricide-tolerant teleost exposed to TFM and niclosamide
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38. A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data
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41. RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
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42. Controlling False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data
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43. Whole-Genome Bisulfite Sequencing (WGBS) Analysis of Gossypium hirsutum under High-Temperature Stress Conditions
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44. Phenotype prediction in plants is improved by integrating large-scale transcriptomic datasets
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45. Biclustering of High-throughput Gene Expression Data with Bicluster Miner
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46. Pan-transcriptomics and its applications
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47. Molecular Biodiversity Convergence with Biogeography and Ethnobotany of Rare and Endangered Medicinal Plants from Northern Vietnam
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48. Discovering common pathogenetic processes between COVID-19 and tuberculosis by bioinformatics and system biology approach
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49. Direct experimental manipulation of intestinal cells in Ascaris suum , with minor influences on the global transcriptome
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50. A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing Data
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51. Underutilised and Neglected Crops: Next Generation Sequencing Approaches for Crop Improvement and Better Food Security
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52. Gene expression profile suggesting immunological dysregulation in two Brazilian Bloom's syndrome cases
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53. Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
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54. Systems-Based Approach to the Analyses of Plant Functions: Conceptual Understanding, Implementation, and Analysis
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55. Large scale maximum average power multiple inference on time‐course count data with application to RNA‐seq analysis
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56. Network module-based model in the differential expression analysis for RNA-seq
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57. Systems Genetics of Complex Diseases Using RNA-Sequencing Methods
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58. multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions
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60. Introduction to Statistical Methods for MicroRNA Analysis
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61. Screening for Differentially Expressed Genes: Are Multilevel Models Helpful?
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63. Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition
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64. DegPack: A web package using a non-parametric and information theoretic algorithm to identify differentially expressed genes in multiclass RNA-seq samples
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65. Integration of small RNAs, degradome, and transcriptome sequencing provides insights into the differences between Shizhu ginseng and Yuan ginseng
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66. Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study
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67. A combined approach with gene-wise normalization improves the analysis of RNA-seq data in human breast cancer subtypes
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68. Deep Transcriptome Profiling of Ovarian Cancer Cells Using Next-Generation Sequencing Approach
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69. DElite: a tool for integrated differential expression analysis
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70. Inferring Interaction Networks from Transcriptomic Data: Methods and Applications
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71. Statistical modeling for differential transcriptome analysis using RNA-Seq technology
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72. Computational Methods for Quality Check, Preprocessing and Normalization of RNA-Seq Data for Systems Biology and Analysis
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73. Adjusted Sample Size Calculation for RNA-seq Data in the Presence of Confounding Covariates
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74. Analysis Considerations for Utilizing RNA-Seq to Characterize the Brain Transcriptome
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75. Challenges Analyzing RNA-Seq Gene Expression Data
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77. Tools for the assessment of epigenetic regulation
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79. Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data
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84. Grouped False-Discovery Rate for Removing the Gene-set-Level Bias of RNA-seq
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85. Differential expression analysis methods for ribonucleic acid-sequencing data
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86. Zero-Inflated Models for RNA-Seq Count Data
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87. Transcriptome Analysis Throughout RNA-seq
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88. Expression of odorant co-receptor Orco in tissues and development stages of Glossina morsitans morsitans, Glossina fuscipies fuscipies and Glossina pallidipies
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93. Detecting differential expression from RNA-seq data with expression measurement uncertainty
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