genomic-data-analysis

There are 10 repositories under genomic-data-analysis topic.

FunctionLab / selene
a framework for training sequence-level deep learning networks
deep-learning genomic-data-analysis sampling-methods
Language:Jupyter Notebook 378
genular / pandora
PANDORA :computer:
machine-learning systems-biology data-science data-visualization data-mining pandora bioinformatics biomarkers clinical-data clustering data-integration drug-discovery genomic-data-analysis microbiome predictive-analytics transcriptomics tsne umap unsupervised-machine-learning
Language:Vue 136
KarchinLab / open-cravat
A modular annotation tool for genomic variants
variant-annotations variant-annotation variant-analysis genomics genomic-data-analysis bioinformatics bioinformatics-pipeline bioinformatics-tool annotation-tool python python3 javascript
Language:JavaScript 119
MicrobeTrace
CDCgov / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics epidemiology network-visualization hiv cdc pathogens phylogenetics phylogenetic-trees phylogeny phylogenomics genomics genomics-visualization genomic-data-analysis sequence-alignment
Language:TypeScript 92
kishwarshafin / helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
genome-assembly genomic-data-analysis human-genetics genome-scale-models oxford-nanopore genome-analysis genome-sequencing genomes genomics
Language:Python 70
muellan / metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq fasta fastq dna-sequences genomic-data-analysis classification bioinformatics bioinformatics-tool bioinformatics-algorithms short-read-mapper long-reads
Language:C++ 59
thierrygosselin / radiator
RADseq Data Exploration, Manipulation and Visualization using R
radseq radseq-data imputation genotype-likelihoods filter genetics missingness outliers genomics genomic-data-analysis genomics-visualization gbs genotyping-by-sequencing visualization outliers-detection heterozygosity paralogs artifacts-detection batch-effects normalization
Language:HTML 59
zhaoxiaofei / bindash
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
big-data dimensionality-reduction bioinformatics genomic-data-analysis locality-sensitive-hashing
Language:C++ 59
bobeobibo / phigaro
Phigaro is a scalable command-line tool for predicting phages and prophages
bioinformatics bioinformatics-tool bioinformatics-pipeline bioinformatics-analysis biological-data-analysis phage phages prophage genomics genomic-data-analysis genomic-regions
Language:HTML 51
thierrygosselin / stackr
stackr: an R package to run stacks software pipeline
radseq rad genotype-likelihoods filter genetics genomics genomic-data-analysis genomics-visualization radseq-data gbs genotyping-by-sequencing stackr
Language:HTML 29
jakublipinski / build-deepsea-training-dataset
Build DeepSea training dataset from raw data
genomic-data-analysis
Language:Python 26
graphsim
TomKellyGenetics / graphsim
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
r-stats igraph-networks simulated-data graph-algorithms package joss genetics gene-expression gene-regulatory-networks benchmarking simulation-modeling genomics genomic-data-analysis ngs-analysis
Language:R 24
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 ec2 ngs snakemake wgs giab ephemeral scaling budgeting genomic-data-analysis human-genome informatics parallel-cluster scalable slurm snv-call cwl
Language:WDL 23
VolcaNoseR
JoachimGoedhart / VolcaNoseR
Shiny app for making and annotating Volcano plots
volcano ggplot2 shinyapp shiny proteomics-data-analysis genomic-data-analysis dataviz
Language:R 23
rjdkmr / gcMapExplorer
Genome Contact Map Explorer - gcMapExplorer. Visit:
genomic-data-analysis hi-c bioinformatics
Language:Python 21
laurentnoe / yass
genomic alignment similarity search tool
sequence-alignment spaced-seed dna-sequences fasta-sequences fasta genomic-data-analysis blastn blast-search sequence-alignments align-dna-sequences
Language:C 18
CBIIT / Misteli-Lab-CCR-NCI
Collection of statistical scripts, image analysis workflows, data used in publications by the Misteli Lab.
knime r cancer biology biological-data-analysis image-analysis genomic-data-analysis workflow misteli-lab deep learning keras tensorflow
Language:HTML 17
annsql
ArpiarSaundersLab / annsql
The AnnSQL package enables SQL based queries on AnnData objects.
anndata h5ad single-cell sql genomic-data-analysis annsql
Language:Python 16
shilab / DP-MIA
Differential Privacy Protection against MembershipInference Attack on Machine Learning for Genomic Data
differential-privacy membership-inference-attack genetic-privacy machine-learning genomic-data-analysis
Language:Python 16
xinglab-ai / genomap
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
bioinfomatics-pipeline bioinformatics bioinformatics-tool deep-learning genomic-data-analysis genomics genomics-visualization single-cell tabular-data biomarker-discovery biomarkers classification-algorithm data-classification multi-omic-integration regression-algorithms trajectory-inference visualization cell-annotation
Language:Python 16
gdurif / pCMF
pCMF R package
statistics r data-visualization matrix-factorization genomic-data-analysis single-cell-analysis gene-expression
Language:C++ 14
bernatgel / regioneR
An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests
bioconductor rstats randomization permutation-test genome genomic-regions genomic-data-analysis bioinformatics
Language:R 13
AABoyles / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics epidemiology network-graph hiv cdc pathogens phylogenetics phylogenetic-trees phylogeny phylogenomics network-visualization network-analysis genomics genomics-visualization genomic-data-analysis sequence-alignment
Language:HTML 12
biodata-fun / htslib_howto
Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts
htslib c sam vcf-files cram-files sam-files bam-files genomic-data-analysis fastq-files
Language:C 11
Poissonfish / iPat
iPat allows you to perform GWAS and GS with drags and clicks!
gwas gui genome-analysis genomics genomic-data-analysis gene-prediction ipat analysis genome association-studies vcf hapmap
Language:Java 11
fjdf / slaMEM
Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array
dna sequencing genome-analysis genomic-data-analysis genomics-visualization mem mummer maximal-exact-matches
Language:C 10
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 rnaseq-analysis somatic-variants variant-calling dockerfile genomic-data-analysis nextflow-pipeline transcriptome-analysis differential-expression
Language:Nextflow 9
CEA-LIST / sgntx
iDASH 2017 competition, track 2 winning team solution
intel sgx idash genomic-data-analysis genomics intel-sgx
Language:Rust 8
WGCA
icaromsc / WGCA
JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes
genomic-islands prophages virulence-genes resistome comparative-genomics genomic-data-analysis bioinformatics-workflow snakemake
Language:Python 8
ishamada / bioiX
PCA on Genotypes
bioinformatics-pipeline computational-biology genomic-data-analysis genomics workflow machine-learning-algorithms
Language:Python 8
mt1022 / gppy
[G]enomic [P]ositioning with [Py]thon
bioinformatics bioinformatics-tool command-line-tool genomic-data-analysis genomics python3
Language:Python 8
grur
thierrygosselin / grur
grur: an R package tailored for RADseq data imputations
genomics genomics-visualization genomic-data-analysis imputation radseq radseq-data gbs machine-learning random-forest boosting-algorithms pca-analysis missing-data
Language:R 7
bcgsc / ntRoot
🌳 Human ancestry inference from genomic data
ancestry ancestry-inference ancestrydna snv snv-call genome genome-assembly genomic-data genomic-data-analysis sequencing-data
Language:Python 6
linas / biome-distribution
Research into statistical distributions of genomes, proteomes and reactomes
genomic-data-analysis genomics-visualization proteomics proteogenomics reactome reactome-pathway
Language:Scheme 6
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
Language:Jupyter Notebook 6
pfeiferd / genestrip
Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species
bioinformatics genomes genomic-data-analysis high-performance kmer-counting kraken2 krakenuniq metagenomic-analysis metagenomic-classification pathogen-genomics command-line-tool java
Language:Java 6