Internal and external normalization of nascent RNA sequencing run-on experiments
In experiments with significant perturbations to transcription, nascent RNA sequencing protocols are dependent on external spike-ins for reliable...
A longitudinal single-cell atlas of treatment response in pediatric AML
Pediatric acute myeloid leukemia (pAML) is characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains understudied in pediatric patients. Researchers at the Michael Smith Genome Sciences Centre used single-cell ...
NORMSEQ – a tool for evaluation, selection and visualization of RNA-Seq normalization methods
RNA-sequencing has become one of the most used high-throughput approaches to gain knowledge about the expression of all different RNA subpopulations. However, technical artifacts, either introduced during library preparation and/or data analysis, can influence the detected RNA expression levels. A ...
Maximizing the potential of high-throughput next-generation sequencing through precise normalization
Next-generation sequencing technologies have enabled many advances across diverse areas of biology, with many benefiting from increased sample size. Although the cost of running next-generation...
How to choose normalization methods (TPM/RPKM/FPKM) for mRNA expression
Why do mRNA expression values need to be normalized? The unification of mRNA expression value measurements across studies, or the normalization of mRNA data, is a significant problem in biomedical and life science research. The abundance of transcripts is measured ...
RUV-III – removing unwanted variation from large-scale RNA sequencing data
Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA sequencing (RNA-seq)...
Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data
Constructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module identification, gene function prediction, and disease-gene...
Normalized counts performs better than TPM, FPKM for hierarchical clustering of replicate RNA-Seq samples
In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for...
SMIXnorm – fast and accurate RNA-Seq data normalization for FFPE Samples
RNA-sequencing (RNA-seq) provides a comprehensive quantification of transcriptomic activities in biological samples. Formalin-Fixed Paraffin-Embedded (FFPE) samples are collected as part of routine clinical procedure, and are the most...
BatchBench – flexible comparison of batch correction methods for single-cell RNA-seq
As the cost of single-cell RNA-seq experiments has decreased, an increasing number of datasets are now available. Combining newly generated and publicly accessible datasets is challenging due to non-biological signals, commonly known as batch effects...
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- BAP-seq – bioorthogonal masked acylating agents for proximity-dependent RNA labelling
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