[PDF][PDF] edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets
Abstract edgeR is an R/Bioconductor software package for differential analyses of
sequencing data in the form of read counts for genes or genomic features. Over the past 15 …
sequencing data in the form of read counts for genes or genomic features. Over the past 15 …
[HTML][HTML] limma powers differential expression analyses for RNA-sequencing and microarray studies
Abstract limma is an R/Bioconductor software package that provides an integrated solution
for analysing data from gene expression experiments. It contains rich features for handling …
for analysing data from gene expression experiments. It contains rich features for handling …
Taurine deficiency as a driver of aging
Aging is associated with changes in circulating levels of various molecules, some of which
remain undefined. We find that concentrations of circulating taurine decline with aging in …
remain undefined. We find that concentrations of circulating taurine decline with aging in …
Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases
MTN Yarnall, EI Ioannidi, C Schmitt-Ulms… - Nature …, 2023 - nature.com
Programmable genome integration of large, diverse DNA cargo without DNA repair of
exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We …
exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We …
[HTML][HTML] MYB orchestrates T cell exhaustion and response to checkpoint inhibition
C Tsui, L Kretschmer, S Rapelius, SS Gabriel… - Nature, 2022 - nature.com
CD8+ T cells that respond to chronic viral infections or cancer are characterized by the
expression of inhibitory receptors such as programmed cell death protein 1 (PD-1) and by …
expression of inhibitory receptors such as programmed cell death protein 1 (PD-1) and by …
A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast
To examine global changes in breast heterogeneity across different states, we determined
the single‐cell transcriptomes of> 340,000 cells encompassing normal breast, preneoplastic …
the single‐cell transcriptomes of> 340,000 cells encompassing normal breast, preneoplastic …
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences
Motivation In RNA-seq differential expression analysis, investigators aim to detect those
genes with changes in expression level across conditions, despite technical and biological …
genes with changes in expression level across conditions, despite technical and biological …
Early precursor T cells establish and propagate T cell exhaustion in chronic infection
DT Utzschneider, SS Gabriel, D Chisanga… - Nature …, 2020 - nature.com
CD8+ T cells responding to chronic infections or tumors acquire an 'exhausted'state
associated with elevated expression of inhibitory receptors, including PD-1, and impaired …
associated with elevated expression of inhibitory receptors, including PD-1, and impaired …
[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 …
Interferon-ε is a tumour suppressor and restricts ovarian cancer
High-grade serous ovarian cancers have low survival rates because of their late
presentation with extensive peritoneal metastases and frequent chemoresistance, and …
presentation with extensive peritoneal metastases and frequent chemoresistance, and …