Computational methods for strain-level microbial detection in colony and metagenome sequencing data

C Anyansi, TJ Straub, AL Manson, AM Earl… - Frontiers in …, 2020‏ - frontiersin.org
Metagenomic sequencing is a powerful tool for examining the diversity and complexity of
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …

RNA sequencing data: hitchhiker's guide to expression analysis

K Van den Berge, KM Hembach… - Annual Review of …, 2019‏ - annualreviews.org
Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …

Differential analysis of RNA-seq incorporating quantification uncertainty

H Pimentel, NL Bray, S Puente, P Melsted, L Pachter - Nature methods, 2017‏ - nature.com
Abstract We describe sleuth (http://pachterlab. github. io/sleuth), a method for the differential
analysis of gene expression data that utilizes bootstrap** in conjunction with response …

Pooled CRISPR screening with single-cell transcriptome readout

P Datlinger, AF Rendeiro, C Schmidl, T Krausgruber… - Nature …, 2017‏ - nature.com
CRISPR-based genetic screens are accelerating biological discovery, but current methods
have inherent limitations. Widely used pooled screens are restricted to simple readouts …

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

C Soneson, MI Love, MD Robinson - F1000Research, 2016‏ - pmc.ncbi.nlm.nih.gov
High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the
transcriptome of cells. Many transcriptomic studies aim at comparing either abundance …

RNA sequencing and analysis

KR Kukurba, SB Montgomery - Cold Spring Harbor Protocols, 2015‏ - cshprotocols.cshlp.org
RNA sequencing (RNA-Seq) uses the capabilities of high-throughput sequencing methods
to provide insight into the transcriptome of a cell. Compared to previous Sanger sequencing …

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

MI Love, W Huber, S Anders - Genome biology, 2014‏ - Springer
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 …

Differential analysis of gene regulation at transcript resolution with RNA-seq

C Trapnell, DG Hendrickson, M Sauvageau… - Nature …, 2013‏ - nature.com
Differential analysis of gene and transcript expression using high-throughput RNA
sequencing (RNA-seq) is complicated by several sources of measurement variability and …

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Nature biotechnology, 2014‏ - nature.com
We present primary results from the Sequencing Quality Control (SEQC) project,
coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life …

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

S Anders, DJ McCarthy, Y Chen, M Okoniewski… - Nature protocols, 2013‏ - nature.com
RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in
many areas of biology, including studies into gene regulation, development and disease. Of …