Useful R-scripts by edert

Diagnostic performance of HPV-DeepSeek, a hybrid capture whole genome sequencing liquid biopsy for HPV-associated cancers

Leveraging WES short reads for PAN-EXOME creation and analysis.

Análisis genómicos y transcriptómicos con plataforma NGS

Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).

Python scripts for design of 5'/3' RACE-based NGS panels, and the following data analysis

A python package storing different tools for different NGS operations

TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time

A genetic sequence analysis on calculating the GC contents and CpG deficiencies on multiple coronaviruses (SAR-CoV, SAR-CoV-2, MERS-CoV and 2 two bat derived SARS-like coronaviruses) to see which coronavirus has the most potentially effective mechanism to escape the anti-virus activities on human bodies.

CRISPRSeqSim is a tool that simulates results of CRISPR/cas editing fragments target sequencing.

Next-generation Sequencing workflows

Aggregation of QC metrics and outlier nomination for multi-sample studies

Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"

Protein Analysis and Classifier Toolkit

Example files for Benin NGS capacity building project

CAYA Analysis

a shiny frontend for the nextflow-bcl pipeline

Code and scripts used for Worth et al. 2022: "Receptor editing constrains development of phosphatidyl choline-specific B cells in VH12-transgenic mice".

Bioinformatics is a field of information technology and biological science, which use to managing, storing and analyzing these biological data such as DNA, RNA and protein, In this repository I'm use python to create various types of program for analyzing biological data