data-analysis

Confirming genotypes by visualizing mutations from RNAseq data

Kazu Nozue / 2019-01-08
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RNAseq is a powerful tool for transcriptome analysis. It is also useful for genotyping (for example, 1). Here I demonstrated an example of confirmation of genotype used for RNAseq. There are some unavoidable errors due to unexpected mistakes in many steps (eg. contamination of seeds, contamination …
data-analysis

VennDiagram with differentially expressed genes

Kazu Nozue / 2018-12-28
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The last time I posted how to draw a VennDiagram with a simulated data. This time I would like to explain how to draw a VennDiagram from differentially expressed genes (DEGs). […] library(limma) library(tidyverse) ## ── Attaching packages …
data-analysis

List to data frame in R tidyverse

Kazu Nozue / 2018-12-20
Converting list object to a data frame object is common in R. There are many ways and here is another way using tidyverse packages. […] This is an efficient implementation of the common pattern of do.call(rbind, dfs) or do.call(cbind, dfs) for binding many data frames into one (cited from …
data-analysis

Annotating sequences by benchling.com

Kazu Nozue / 2018-12-06
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Annotating sequences is critical for making a construct in molecular biology. Benchling.com is a powerful tool for automating the annotation process. This example explains how to label “2x35S promoter” region in sequences of interest. […] benchling.com plasmid annotation (step1) […] …
data-analysis

Interactive app for time-course data of your kids' meet scores

Kazu Nozue / 2018-11-06
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Shiny package in R language can create a fantastic application in interactive mode using a browser (for free!). In an example below, you can download data file for four years of figure records in US junior olympics of synchronized swimming (public available data from USA synchro web site, compiled …
data-analysis

Another plant defense hormone is required for responses to light in plant

Kazu Nozue / 2018-10-26
Plants use light as energy source as well as signals for environmental signal changes. Under the canopy shade phtosynthesis activity is reduced, therefore plants responded to existance of neighboring plants that causes near future crisis, such as growing taller and flowering earlier to produce seeds …