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 1.3.0 ── ## ✓ ggplot2 3.3.3 ✓ purrr 0.3.4 ## ✓ tibble 3.0.4 ✓ dplyr 1.0.2 ## ✓ tidyr 1.1.2 ✓ stringr 1.4.0 ## ✓ readr 1.4.0 ✓ forcats 0.5.0 ## ──…

data analysis

VennDiagram

Kazu Nozue / 2018-10-15

# library(limma) library(tidyverse) library(ggforce) set.seed((123)) mydata <- data.frame(A = rbinom(100, 1, 0.8), B = rbinom(100, 1, 0.7), C = rbinom(100, 1, 0.6)) %>% mutate_all(., as.logical) # drawing circle df.venn <- data.frame(x = c(0, 0.866, -0.866), y = c(1, -0.5, -0.5), labels =…

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 1.3.0 ── ## ✓ ggplot2 3.3.3 ✓ purrr 0.3.4 ## ✓ tibble 3.0.4 ✓ 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…

data analysis

Over-representation analysis 4: heatmap visualization

Kazu Nozue / 2018-09-27

Similar analysis was found in Guangchuang Yu bioconductor vignettes page. library(tidyverse);library(ShortRead);library(goseq);library(GO.db);library("annotate") ## Warning: package 'S4Vectors' was built under R version 3.6.3 ## Warning: package 'GenomeInfoDb' was built…