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cqn [35] is a normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. EDASeq [36] is a Bioconductor package to perform GC-Content Normalization for RNA-Seq Data. GeneScissors A comprehensive approach to detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment.
Strand-seq overcomes limitations of methods based on whole genome amplification for genetic variant calling: Since Strand-seq does not require reads (or read pairs) transversing the boundaries (or breakpoints) of CNVs or copy-balanced structural variant classes, it is less susceptible to common artefacts of single-cell methods based on whole ...
Small RNA sequencing (Small RNA-Seq) is a type of RNA sequencing based on the use of NGS technologies that allows to isolate and get information about noncoding RNA molecules in order to evaluate and discover new forms of small RNA and to predict their possible functions.
Single-cell RNA sequencing (scRNA-Seq) provides the expression profiles of individual cells. Although it is not possible to obtain complete information on every RNA expressed by each cell, due to the small amount of material available, patterns of gene expression can be identified through gene clustering analyses. This can uncover the existence ...
There is so far no standardized technique to generate single-cell data: all methods must include cell isolation from the population, lysate formation, amplification through reverse transcription and quantification of expression levels. Common techniques for measuring expression are quantitative PCR or RNA-seq. [6]
Perturb-seq (also known as CRISP-seq and CROP-seq) refers to a high-throughput method of performing single cell RNA sequencing (scRNA-seq) on pooled genetic perturbation screens. [ 1 ] [ 2 ] [ 3 ] Perturb-seq combines multiplexed CRISPR mediated gene inactivations with single cell RNA sequencing to assess comprehensive gene expression ...
By minimizing these systematic variations, true biological differences can be found. To determine whether normalization is needed, one can plot Cy5 (R) intensities against Cy3 (G) intensities and see whether the slope of the line is around 1. An improved method, which is basically a scaled, 45 degree rotation of the R vs. G plot is an MA-plot. [4]
A small conditional RNA (scRNA) is a small RNA molecule or complex (typically less than approximately 100 nt) engineered to interact and change conformation conditionally in response to cognate molecular inputs so as to perform signal transduction in vitro, in situ, or in vivo.