microRNA validation using Spark framework

A QC pipeline for SVs calls based on coverage and SNP calls

Data science project, analysing NGS data from a binding study,

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.

miscellaneous stand-alone basic utilities for genomics and genomics-adjacent operations (share with lab mates)

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

Pipeline para montagem direcionada (gene-a-gene) a partir de leituras pareadas.

This repository covers research paper implementations in the field of Genomics, Next Generation Sequencing, Bioinformatics and Machine Learning.

An assessment of the species diversity and disease potential of Pythium communities in Europe

Here is my participation to the 2024 edition of the HackBio Internship (AMR in cancer track).

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.

Developed a Bash-based pipeline for bacterial NGS data analysis, including QC, trimming, alignment, variant calling, and annotation (FastQC, Trimmomatic, BWA, Samtools, bcftools, SnpEff).

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

Variant calling pipeline (Snakemake workflow)

A portfolio of Nupur Upadhyay, a BS-MS student at IISER Thiruvananthapuram, Kerala, India.

Personal blog on computational biology and pathology

Detection of unknown genetically modified organisms

List of the filtering criteria of the variants called in samples of Vitis vinifera cv. Tempranillo

This tool is aimed at helping to analyze small to medium vcf files of genotyped individuals.