Analysis of microbial compositions: a review of normalization and differential abundance analysis
H Lin, SD Peddada - NPJ biofilms and microbiomes, 2020 - nature.com
Increasingly, researchers are discovering associations between microbiome and a wide
range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on …
range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on …
RNA-Seq differential expression analysis: An extended review and a software tool
The correct identification of differentially expressed genes (DEGs) between specific
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
Cellular and transcriptional dynamics of human neutrophils at steady state and upon stress
E Montaldo, E Lusito, V Bianchessi, N Caronni… - Nature …, 2022 - nature.com
Traditionally viewed as poorly plastic, neutrophils are now recognized as functionally
diverse; however, the extent and determinants of neutrophil heterogeneity in humans remain …
diverse; however, the extent and determinants of neutrophil heterogeneity in humans remain …
Differential analysis of RNA-seq incorporating quantification uncertainty
Abstract We describe sleuth (http://pachterlab. github. io/sleuth), a method for the differential
analysis of gene expression data that utilizes bootstrapping in conjunction with response …
analysis of gene expression data that utilizes bootstrapping in conjunction with response …
[HTML][HTML] From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for
profiling gene expression. One of the most common aims of RNA-seq profiling is to identify …
profiling gene expression. One of the most common aims of RNA-seq profiling is to identify …
Epigenetic regulation of brain region-specific microglia clearance activity
The rapid elimination of dying neurons and nonfunctional synapses in the brain is carried
out by microglia, the resident myeloid cells of the brain. Here we show that microglia …
out by microglia, the resident myeloid cells of the brain. Here we show that microglia …
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 …
[HTML][HTML] CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
High-dimensional mass and flow cytometry (HDCyto) experiments have become a method
of choice for high-throughput interrogation and characterization of cell populations. Here, we …
of choice for high-throughput interrogation and characterization of cell populations. Here, we …
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
In comparative high-throughput sequencing assays, a fundamental task is the analysis of
count data, such as read counts per gene in RNA-seq, for evidence of systematic changes …
count data, such as read counts per gene in RNA-seq, for evidence of systematic changes …
Human germline heterozygous gain-of-function STAT6 variants cause severe allergic disease
STAT6 (signal transducer and activator of transcription 6) is a transcription factor that plays a
central role in the pathophysiology of allergic inflammation. We have identified 16 patients …
central role in the pathophysiology of allergic inflammation. We have identified 16 patients …