RNA-seq
2025-11-30
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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 1.3.0 ── ## ✓ 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
Over-representation analysis 5: useful tools
Kazu Nozue
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2018-10-07
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…
