genomics-data

There are 3 repositories under genomics-data topic.

• ncbi / datasets

  NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

  genomics-datancbi
  Language:Jupyter Notebook 355
• mixOmics

  mixOmicsTeam / mixOmics

  Development repository for the Bioconductor package 'mixOmics '

  bioconductorgenomicsgenomics-datagenomics-visualizationmultivariate-analysismultivariate-statisticsomicsrr-packager-pkgr-projectrstatsrstats-package
  Language:R 157

• ML-Bioinfo-CEITEC / genomic_benchmarks

  Benchmarks for classification of genomic sequences

  deep-learningdatasetgenomicsgenomics-datatensorflowpytorch
  Language:Jupyter Notebook 109
• DUO

  EBISPOT / DUO

  Ontology for consent codes and data use requirements

  obofoundryontologydatasets-taggedbiomedical-informaticsbiomedical-applicationsgenomics-dataowl
  Language:Makefile 64

• HallLab / pandas-genomics

  Pandas ExtensionDtypes for dealing with genomics data

  genomics-datapandas-extensiondtypes
  Language:Python 47

• ACDBio / AutoMR

  An R script to perform two sample Mendelian randomization screening (with TwoSampleMR) for a custom summary statistic against a set of summary statistics from the IEU GWAS database.

  causalitygenomicsgenomics-datagwasmendelian-randomization
  Language:R 33

• ncherric / Iliad

  ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

  automaticgeneticsgenomics-datasnakemakeworkflowbioinformaticsfastqgenomicsmodularizationcramidatvcf
  Language:Python 28

• ToledoEM / msigdf

  Molecular Signatures Database (MSigDB) in a data frame

  msigdbreference-datagseageneset-enrichmentgenesetstidy-datarr-packagegenesgeneontologygenomicsgenomics-datatidyverse
  Language:HTML 23

• Sentieon / sentieon-dnaseq

  Sentieon DNAseq

  dna-sequencingvariant-callingbioinformatics-pipelinesentieondnaseqgenomics-databwa-memaccelerationgatkgatk4
  Language:Shell 22

• outbreak-info / R-outbreak-info

  R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.

  rstatsrstats-packageepidemiologygenomicsgenomics-visualizationgenomics-data
  Language:R 20

• s1monj / nft-peppers

  Generative Art NFTs from Genomic Data

  cytoscapejsanimejsgenomics-visualizationgenomics-datajavascript
  Language:JavaScript 20

• furkanmtorun / gnomad_python_api

  🧬 gnomAD Python API is used to obtain data from gnomAD (genome aggregation database).

  gnomadgenomicsbioinformatics-databasesgenomics-datagnomad-python-apivariantsgenome-aggregation-database
  Language:Python 19

• IPK-BIT / divbrowse

  A web application for interactive visualization and exploratory data analysis of variant call matrices

  bioinformaticsdata-visualizationvisualizationgenomicsgenomics-analysisgenomics-datagenomics-visualizationgff3principal-component-analysisvcf
  Language:Svelte 16

• kpatel427 / R-scripts

  Miscellaneous R script to wrangle data and generate visualizations

  heatmappheatmapcorrelationvisualizationggplot2ggplot2-geomgenomics-visualizationgenomics-datasplit
  Language:R 16

• theislab / cellrank_reproducibility

  CellRank's reproducibility repository.

  genomics-datamachine-learningreproducible-researchsingle-cell
  Language:Jupyter Notebook 14

• Sentieon / sentieon-dnascope-ml

  Sentieon DNAscope + Machine Learning Model

  variant-callingmachine-learninggenomics-datanext-generation-sequencingdnasentieondnascopegermline-variantsbioinformatics-pipeline
  Language:Shell 12

• BioJulia / ReadDatastores.jl

  Datastores for reads, not your papa's FASTQ files.

  bam-filesbam-formatbioinformaticsbioinformatics-databiojuliabiologyfastqfastq-filesfastq-formatfilesformatgenomicsgenomics-datasam-bamsam-filesam-filessequencingstorage
  Language:Julia 11

• vangiangtran / BWGS

  2024 BreedWheat Genomic Selection pipeline

  genomic-selectiongenomics-datagenomic-predictiongeneticsquantitative-analysiscross-validationbreeding-datastatistical-modelsrcran-r
  Language:R 11

• victorskl / genomic-bigdata-spark

  Genomic BigData Warehousing with Apache Spark and LakeHouse Architecture

  bigdatabioinformaticsdatalakedelta-lakegenomics-datalakehouseparquetsparkspark-sqldatawarehousingcloud-computingcloudnative
  Language:Jupyter Notebook 11

• tseemann / kounta

  🧮 🔢 Generate multi-sample k-mer count matrix from WGS

  kmer-countinggenomics-datamachine-learningdata-sciencegwas
  Language:Perl 10

• histolab / gdc-api-wrapper

  Genomic Data Commons API wrapper

  api-wrapperapitcgagenomics-datatciacancer
  Language:Python 7

• HolubievIllya / Command-Line-Tools-for-Genomic-Data-Science

  This repository contains the answers for coursera 's "Command Line Tools for Genomic Data Science"

  command-line-toolcourse-answerscourseracoursera-answerscoursera-assignmentcoursera-assignment-solutioncoursera-coursecoursera-solutionsdatagengenesgenomicgenomicsgenomics-datalinequiztools
  6

• lakhanp1 / fungal_resources

  R AnnotationDB resources like org.db, tx.db for various fungal species

  genomics-datagenomics-data-setsorgdbtxdbbsgenomefungal-genomes
  Language:R 6

• outbreak-info / python-outbreak-info

  Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info

  covid-19covid-datagenomicsgenomics-datagenomics-visualizationsars-cov-2variants
  Language:Jupyter Notebook 6

• bio-ontology-research-group / STARVar

  STARVar:Symptom based Tool for Automatic Ranking of Variants using evidence from literature and genomes

  text-mininggenomics-datavariant-rankingvariant-priorisation
  Language:Python 5

• HolubievIllya / Bioconductor-for-Genomic-Data-Science

  This repository contains the answers for coursera 's "Bioconductor for Genomic Data Science"

  bioconductorcourse-answerscourseracoursera-answerscoursera-assignmentcoursera-assignment-solutioncoursera-coursecoursera-solutionsdatadata-sciencegengenomicgenomicsgenomics-dataquizrsciencetools
  5

• GenomicsDB / GenomicsDB-R

  Experimental R bindings to the native GenomicsDB library

  genomicsgenomics-datagenomicsdbr
  Language:R 4

• omics-lab / VirusTaxo_Hierarchical

  Implementation of https://doi.org/10.1016/j.ygeno.2022.110414

  bioinformaticsclassificationsupervised-learningpython3genomics-data
  Language:Roff 4

• GenGrim76 / Pareto-Optimal-GDC

  :chart_with_downwards_trend: Disk Storage of Compressed k-mer Dictionaries, with or without Random Access in Main Memory.

  compressiongenomics-datasuccinct-data-structurerandom-access-in-main-memoryalignment-freebioinformaticspareto-optimality
  Language:Java 3

• jajokine / Genomics-and-High-Dimensional-Data

  MITx - MicroMasters Program on Statistics and Data Science - Data Analysis: Statistical Modeling and Computation in Applications - Second Project

  genomicsgenomics-visualizationgenomics-dataclustering-methodsclustering-analysisprincipal-component-analysislogistic-regressionregularizationl1-regularizationl2-regularizationhierarchical-clusteringkmeans-clustering
  Language:Jupyter Notebook 3

• LotharukpongJS / phylomapr

  Get precomputed gene age maps (phylomaps) in R

  bioinformaticsgene-agegenomics-dataphylostratigraphy
  Language:R 3
• HaploDynamics

  remytuyeras / HaploDynamics

  A python library to develop genomic data simulators

  allele-frequenciesgenomics-datahardy-weinberg-equilibriumlinkage-disequilibriumpopulation-geneticspopulation-genomicssimulationsimulatorvcfvcf-filesgwasgwas-datasetdnadna-sequencesgenomicsmicroarray-data
  Language:Python 3

• ArnaudFickinger / LotteryTicket-PyTorch

  Manifestation of the Lottery Ticket Phenomena in supervised, reinforcement and unsupervised learning.

  genomics-datalottery-ticket-phenomenapruningreinforcement-learningunsupervised-learning
  Language:Python 2

• AstraBert / simON-reads

  simON-reads ("Simulate Oxford Nanopore Reads") is a simple yet powerful tool to generate fastq files containing MiniON-like long reads

  artificial-dataautomationbioinformaticsgenomics-datalong-read-sequencingoxford-nanoporetestingthird-generation-sequencing
  Language:Python 2

• biodata-fun / nf_genomics_pipelines

  This repo contains pipeline implemented using the nextflow workflow management system for the analysis of genomics data

  analysisbamcoveragecram-filesgenomicsgenomics-datanextflow-pipelinesnextflow-workflow-managementnf-genomics-pipelines
  Language:Nextflow 2

• NathanSiemers / FauxFlow

  FauxFlow - Analyze Single Cell Genomics Data in a Flow Cytometry Paradigm

  rna-seqshiny-applicationsgenomics-visualizationgenomics-dataflow-cytometryrstatsrshinyrshinyapp
  Language:R 2