Welcome to my repository of bioinformatics analysis scripts. This repository contains a collection of scripts that I've developed for various bioinformatics tasks, including differential expression analysis, transcriptomics, epigenetics and custom downstream analyses.
├── differentialExpression: Analysis of RNA-seq data,
quantification, annotation, differential expression,
enrichment analysis.
├── downstream_analyses: In-depth analysis of processed NGS data,
statistical analysis, data visualization.
├── nf: NEXTFLOW pipeline scripts.
├── genomic_visualization: Genome-wide signal visualization,
metagene profiles, ideograms,
UCSC genome browser.
├── genotypic_data_analysis: Processing SNP variant microarray data,
filtering and annotation.
├── m6A_analysis: Peak calling, m6A prediction,
differential methylation.
├── mapping: Mapping short and long-read NGS data to reference genomes,
processing alignment files, downsampling and normalization.
├── nanopore_analysis: Base-calling of Nanopore long-read data,
signal processing and detection of m6A modifications.
├── quality_control: QC analysis and report generation.
├── quantification: Transcript and gene-level quantification of RNA-seq data.
├── query_databases: Fetching and querying data from public databases.
└── transcriptomics: Transcriptome assembly, differential exon usage.
If you have any questions or suggestions, feel free to reach out to me:
- LinkedIn: Akram Mendez