Projects in Awesome Lists tagged with genomic-data-analysis
A curated list of projects in awesome lists tagged with genomic-data-analysis .
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/simon-frontend
PANDORA :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: 23 Jan 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 May 2025
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: 13 Dec 2024
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: 20 Nov 2024
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: 04 Dec 2024
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: 12 Apr 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: 04 Dec 2024
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/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: 21 Feb 2025
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: 21 Feb 2025
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: 07 May 2025
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: 16 Mar 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: 07 Apr 2025
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/gauravcodepro/genome-analysis-slurm-pbs
slurm and pbs scripts for genome, metagenome, transcriptome analysis.
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomic-data-analysis genomics genomics-visualization
Last synced: 22 Feb 2025
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/gauravcodepro/odd-ratio-estimator
This function will take a data frame of the outbreak and will predict the odd ratios and the specific likelihood of occurrence of the disease in that specific geographical location
genomic-data-analysis genomics-data infectious-disease-models infectious-diseases odds-ratio python risk-analysis risk-assessment risk-management
Last synced: 22 Feb 2025
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: 05 Mar 2025
