RNA-seq
2021-01-07
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data-analysis
Confirming genotypes by visualizing mutations from RNAseq data
Kazu Nozue
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2019-01-08
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
Over-representation analysis 3: GOseq with GO term in non-model organisms
Kazu Nozue
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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
Over-representation analysis 5: useful tools
Kazu Nozue
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2018-10-07
data-analysis
Differential expression analysis with public available sequencing data
Kazu Nozue
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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 1: GOseq with GO terms in unsupported model organisms
Kazu Nozue
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2018-09-26
Over-representation analysis (“enrichment analysis”) of RNA-seq data considering cDNA length effects with unsupported model organisms. […] Among many transcriptome analysis platforms, transcriptome analysis by next-generation sequencing (RNA-seq) has been used widely among model and non-model …
