Bioinformatics on GCP, AWS or Azure

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

Tool to estimate deltas for sequence sets and answer questions about relative contribution

Read-Based Phasing Algorithm with Integrated Multi-Method Support for Enhanced Accuracy

ML phylogenetic inference for non-model organisms with short reads & assemblies

MAGIC - Multimodal Analysis of Genomics, Imaging and Clinical data

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

NLR-Assembler is a command line tool for improving RenSeq Assemblies using linked-read sequencing by 10x Genomics.

Code for the 'DNA Toolkit' YouTube series: Learn Python and how to use it for DNA/RNA manipulation and finding proteins in genome sequences.

A powerful terminal-based bioinformatics tool designed for DNA sequence analysis.

Using NVIDIA Deepmind's Nucleotide Transformer to generate embeddings for yeast genomes.

A class of utilities for processing DNA sequencing reads in computational genomics

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

VCF Analysis Agent using strands agent SDK and bcftools

This repository contains the file codes used to complete the final project for the course Post Genomic Analysis.

Filter DE genes based on log2Folchange, FDR value or both

Mutational signal profiling from somatic variation to detect disrupted mechanisms in somatic cells (typically cancers) using https://github.com/AlexandrovLab/SigProfilerExtractor

Spectra: a tool for repeat-driven sequence visualization

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

Reverse Complement PCR (RC-PCR_ Classification pipeline.