data-analysis

DGE clustering with ggplot2

Kazu Nozue / 2018-10-24

Hierarchical clustering is powerful method to classify gene expression pattern. Here I applied a method develped by an example of plotly. […] # install.packages('ggdendro') library(tidyverse);library(ggdendro);library(plotly) Reading expression value # reading gene expression value …

data-analysis

Over-representation analysis 3: GOseq with GO term in non-model organisms

Kazu Nozue / 2018-10-17

Please prepare […] library(tidyverse);library(readr);library(readxl) ## ── Attaching packages ───────────────────────────────────── tidyverse 1.2.1 ── ## ✔ ggplot2 3.1.0 ✔ purrr 0.2.5 ## ✔ tibble 1.4.2 ✔ dplyr 0.7.7 ## ✔ tidyr 0.8.2 ✔ stringr 1.3.1 ## ✔ readr 1.1.1 ✔ forcats 0.3.0 ## ── …

data-analysis

Merging two branches in Git

Kazu Nozue / 2018-10-12

Here is a simple example using RStudio. […] Initial commit. (“1st commit”) […] 2nd commit (“koi no yokan”) […] 3rd commit (“Tsuki ni nureta futari”) […] 4th commit (“Mayonaka Sugi no koi”) […] Making branch1 …

data-analysis

Over-representation analysis 2: GOseq using custom categories

Kazu Nozue / 2018-10-10

Most updated annotation can be downloaded from TAIR website (for subscribers). I used “TAIR Data 20180630”. library(tidyverse);library(readxl);library(readr) ## ── Attaching packages ───────────────────────────────────── tidyverse 1.2.1 ── ## ✔ ggplot2 3.1.0 ✔ purrr 0.2.5 ## ✔ tibble 1.4.2 ✔ dplyr …

data-analysis

Over-representation analysis 5: useful tools

Kazu Nozue / 2018-10-07

data-analysis

Differential expression analysis with public available sequencing data

Kazu Nozue / 2018-10-01

Please download and modify your input/output file location […] Let’s use published RNA-seq data from Arabidopsis thaliana mutants (npr1-1 and npr4-4D) Ding (2018). library(tidyverse) library(stringr) library(edgeR) Trimming unnecessary sequences from data (such as adaptors) by trimmomatic …