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Computational methods for strain-level microbial detection in colony and metagenome sequencing data
Metagenomic sequencing is a powerful tool for examining the diversity and complexity of
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …
RNA sequencing data: hitchhiker's guide to expression analysis
Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …
regulatory programs are observable. The measurement of transcriptome-wide gene …
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 bootstrap** in conjunction with response …
analysis of gene expression data that utilizes bootstrap** in conjunction with response …
Pooled CRISPR screening with single-cell transcriptome readout
CRISPR-based genetic screens are accelerating biological discovery, but current methods
have inherent limitations. Widely used pooled screens are restricted to simple readouts …
have inherent limitations. Widely used pooled screens are restricted to simple readouts …
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the
transcriptome of cells. Many transcriptomic studies aim at comparing either abundance …
transcriptome of cells. Many transcriptomic studies aim at comparing either abundance …
RNA sequencing and analysis
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 …
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
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 …
Differential analysis of gene regulation at transcript resolution with RNA-seq
Differential analysis of gene and transcript expression using high-throughput RNA
sequencing (RNA-seq) is complicated by several sources of measurement variability and …
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 …
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
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 …
many areas of biology, including studies into gene regulation, development and disease. Of …