https://github.com/FunctionLab/selene

a framework for training sequence-level deep learning networks

deep-learning genomic-data-analysis sampling-methods

Last synced: 19 Apr 2025

https://github.com/genular/pandora

PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:

bioinformatics biomarkers clinical-data clustering data-integration data-mining data-science data-visualization drug-discovery genomic-data-analysis machine-learning microbiome pandora predictive-analytics systems-biology transcriptomics tsne umap unsupervised-machine-learning

Last synced: 03 Apr 2025

https://github.com/KarchinLab/open-cravat

A modular annotation tool for genomic variants

annotation-tool bioinformatics bioinformatics-pipeline bioinformatics-tool genomic-data-analysis genomics javascript python python3 variant-analysis variant-annotation variant-annotations

Last synced: 16 Nov 2025

https://github.com/karchinlab/open-cravat

A modular annotation tool for genomic variants

annotation-tool bioinformatics bioinformatics-pipeline bioinformatics-tool genomic-data-analysis genomics javascript python python3 variant-analysis variant-annotation variant-annotations

Last synced: 16 May 2025

https://github.com/kishwarshafin/helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

genome-analysis genome-assembly genome-scale-models genome-sequencing genomes genomic-data-analysis genomics human-genetics oxford-nanopore

Last synced: 17 Jan 2026

https://github.com/thierrygosselin/radiator

RADseq Data Exploration, Manipulation and Visualization using R

artifacts-detection batch-effects filter gbs genetics genomic-data-analysis genomics genomics-visualization genotype-likelihoods genotyping-by-sequencing heterozygosity imputation missingness normalization outliers outliers-detection paralogs radseq radseq-data visualization

Last synced: 11 Aug 2025

https://github.com/muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

bioinformatics bioinformatics-algorithms bioinformatics-tool classification dna-sequences fasta fastq genome genomic-data-analysis long-reads metagenomes metagenomic-analysis metagenomic-classification metagenomic-data metagenomics ncbi-refseq read-mapping refseq short-read-mapper taxonomy

Last synced: 09 Apr 2025

https://github.com/bobeobibo/phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool biological-data-analysis genomic-data-analysis genomic-regions genomics phage phages prophage

Last synced: 09 Jul 2025

https://github.com/thierrygosselin/stackr

stackr: an R package to run stacks software pipeline

filter gbs genetics genomic-data-analysis genomics genomics-visualization genotype-likelihoods genotyping-by-sequencing rad radseq radseq-data stackr

Last synced: 30 Jul 2025

https://github.com/daylily-informatics/daylily

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

aws bioinformatics bioinformatics-pipeline budgeting cwl ec2 ephemeral genomic-data-analysis giab human-genome informatics ngs parallel-cluster scalable scaling slurm snakemake snv-call wgs

Last synced: 19 Jun 2025

https://github.com/JoachimGoedhart/VolcaNoseR

Shiny app for making and annotating Volcano plots

dataviz genomic-data-analysis ggplot2 proteomics-data-analysis shiny shinyapp volcano

Last synced: 30 Jul 2025

https://github.com/xinglab-ai/genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

bioinfomatics-pipeline bioinformatics bioinformatics-tool biomarker-discovery biomarkers cell-annotation classification-algorithm data-classification deep-learning genomic-data-analysis genomics genomics-visualization multi-omic-integration regression-algorithms single-cell tabular-data trajectory-inference visualization

Last synced: 08 Mar 2026

https://github.com/aaboyles/microbetrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

bioinformatics cdc epidemiology genomic-data-analysis genomics genomics-visualization hiv network-analysis network-graph network-visualization pathogens phylogenetic-trees phylogenetics phylogenomics phylogeny sequence-alignment

Last synced: 25 Feb 2026

https://github.com/AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

bioinformatics cdc epidemiology genomic-data-analysis genomics genomics-visualization hiv network-analysis network-graph network-visualization pathogens phylogenetic-trees phylogenetics phylogenomics phylogeny sequence-alignment

Last synced: 13 Apr 2025

https://github.com/inmegen/pipelines_inmegen

Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.

bioinformatics differential-expression dockerfile genomic-data-analysis nextflow-pipeline rnaseq-analysis somatic-variants transcriptome-analysis variant-calling

Last synced: 08 Apr 2026

https://github.com/cea-list/sgntx

iDASH 2017 competition, track 2 winning team solution

genomic-data-analysis genomics idash intel intel-sgx sgx

Last synced: 05 Apr 2026

https://github.com/linas/biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes

genomic-data-analysis genomics-visualization proteogenomics proteomics reactome reactome-pathway

Last synced: 03 Jan 2026

https://github.com/bcgsc/ntroot

🌳 Human ancestry inference from genomic data

ancestry ancestry-inference ancestrydna genome genome-assembly genomic-data genomic-data-analysis sequencing-data snv snv-call

Last synced: 27 Jul 2025

https://github.com/nathadriele/biophenotype-rag

This project implements a RAG (Retrieval-Augmented Generation) application to answer questions about phenotypes using biological and genomic data. The pipeline integrates information retrieval with response generation via language models (LLM), facilitating accurate analysis of phenotypic data.

anaconda genomic-data-analysis grafana groq jupyter-notebook langchain llm monitoring phenotypes pinecone pipeline-ingestion postgresql prefect pytest rag sql streamlit

Last synced: 31 Aug 2025

https://github.com/tanaylab/misha

Genomic data analysis suite

genomic-data-analysis

Last synced: 25 May 2026

https://github.com/hannahvmeyer/limmboanalysis

genomic-data-analysis linear-mixed-models python

Last synced: 17 May 2026

https://github.com/adeschen/consensusseeker

This R package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. Tested on ChIP-Seq peaks and nucleosome positions.

chip-seq-analysis genomic-data-analysis nucleosome-positioning r-package

Last synced: 18 Mar 2025

https://github.com/nathadriele/genotrack-genomic-phenotypic-data-validation-system

GenoTrack é um sistema teste para controle, validação e visualização de dados genéticos e fenotípicos de pacientes, voltado para estudos de genômica.

automated-testing bdd-tests css3 e2e-tests framework genomic-data-analysis genotrack html5 javascript newman-reporter phenotypic-data postgresql postman robot rspec ruby-on-rails simplecov

Last synced: 13 Apr 2026

https://github.com/matthew-mosior/basic-variant-tools

Command-line toolkit for genomic datasets.

bioinformatics-tool composable genomic-data-analysis haskell haskell-stack optparse-applicative somatic-variants

Last synced: 29 Jun 2026

https://github.com/vaishnavipaithane/genomic-data-and-management-analysis

This miniproject is part of 'Fundamentals of Python Programming' virtual internship conducted by Nyberman Bioinformatics, Europe.

genomic-data-analysis genomics-visualization python spyder

Last synced: 30 Jun 2026

https://github.com/ikergarcia1996/gene2tab

This script is used to convert the output of ABRICATE tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.

abricate genomic-data-analysis genomics genomics-visualization table

Last synced: 08 Apr 2025

https://github.com/nigms/16srrna-microbial-analysis

This repository provides a cloud-based learning module for microbial analysis of 16S rRNA sequencing data. It covers principles, data preprocessing, taxonomic classification, and diversity analysis using R and AWS SageMaker.

16srna aws-sagemaker bioinformatics computational-biology dada2 docker-container genomic-data-analysis ggplot2 high-throughput-sequencing microbiome phyloseq r-programming sequence-processing taxonomic-classification

Last synced: 17 Jun 2025

https://github.com/danielperez9430/bluegen

Personal genomics from WGS: PRS, ClinVar, pharmacogenomics, ancestry & wellbess reports. Offline, free and powered by PRSKit.

genomic-data-analysis genomics health-report pharmacogenomics polygenic-risk-scores population-genetics prs vcf-automation wgs

Last synced: 24 Jun 2026