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The QC report summarizes the passage, failure, warning, etc. for each item.Basic statisticsBasic statistics contain basic statistical information such as file format, encoding, sequence number, number of poor quality flags in FASTQ, sequence length, and GC ratio.For good data, poor quality sequences are small, uniform sequence length is shown,The overall GC content of the analyzed organism shoul..

Key packages and functionsGene expression analysis:DESeq2: Differential expression analysis of RNA-Seq data.EdgeR: Differential gene expression analysis.Gene sequencing:Biostrings: manipulation and analysis of DNA, RNA, and protein sequence data.ShortRead: Next Generation Sequencing (NGS) Data Analysis.Functional interpretation:ClusterProfiler: Gene Ontology (GO) and Pathway Analysis.TopGO: Anal..

1. Data type conversion and filteringTransform the data types of columns required for data analysis.For example, POS can be converted to integer and QUAL to float.# Data type conversiondf['POS'] = df['POS'].astype(int)df['QUAL'] = df['QUAL'].astype(float)df['AF'] = df['AF'].apply(lambda x: float(x.split(',')[0]))# Filtering only high-quality variationshigh_quality_variants = df[df['QUAL'] >= 30]..

statisics and RLinear models and Matrix Algebra

Bioconductor- R package providing system for genome analysis (many package collection)- You can check the information on each package on the bioconductor website.- Provide analysis tool and example data▶ INSTALLATION METHOD# 설치if (!requireNamespace("BiocManager", quietly = TRUE))    install.packages("BiocManager")# 기본 package 다운BiocManager::install() # 특정 package 다운BiocManager::install(원하는 packa..

https://greendaygh.github.io/Rstat2020/

- bedtools - samtools - bcftools -HTSlib - sickle - bwa-mem - gatk

BLAST (Basic Local Alignment Search Tool) NCBI database A bioinformatics tool that compares a query sequence (nucleic acid or protein) to the NCBI sequence database to find similar sequences.