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Toolkit for automated and rapid discovery of structural variants

DeepSeek LLM: Let there be answers

An Integrated Analysis Tool for Copy Number Variation on Whole Exome Sequencing

The snakemake workflow for whole-exome sequencing analysis and generating vcf files

Phenotype driven gene prioritization for HPO

PhenoGPT2 is an advanced phenotype recognition model, leveraging the robust capabilities of large language models.

A genomics-proteomics toolkit

CNV-Z is a copy number caller software for detection of copy number variation from next generation sequencing data.

Whole exome sequencing pipeline for inherited diseases

prediction model for functional UTR variants

The Bioinformatician’s Interactive Lab Notebook (BILN) is a smart, dynamic system for tracking experiments, datasets, and workflows. Designed for bioinformaticians, it ensures reproducibility, stru…

My Top Go-To Protocol Resources for Bioinformatics, Computational Biology & Omics

Tools for working with genomic and high throughput sequencing data.

Fastq preprocessor with optional contamination removal implemented in NextFlow. Supports short and long reads.

PRP: Pathogenic Risk Prediction for Rare Nonsynonymous Single Nucleotide Variants

Provides HTML reports with detailed coverage analysis for clinical NGS data.

A companion R package for the MicrobiomeAnalyst web server

🔬 Assemble large genomes using short reads

A pathway profiling tool designed for traversing metabolic pathway graphs, identifying most complete paths based on an evaluation set of KEGG orthologs (KO), and generalized for internal usage with…

structural variant calling and genotyping with existing tools, but, smoothly.

lumpy: a general probabilistic framework for structural variant discovery

"re-Searcher" is a toolbox aimed to simplify the task for genomics data mining from big VCF files.