a framework for training sequence-level deep learning networks
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- Jupyter Notebook
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genomic-data-analysis
Here are 148 public repositories matching this topic...
A modular annotation tool for genomic variants
javascript python bioinformatics genomics python3 bioinformatics-pipeline annotation-tool variant-annotations variant-annotation variant-analysis genomic-data-analysis bioinformatics-tool
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- JavaScript
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics genomics phylogenetic-trees phylogenetics epidemiology network-visualization hiv cdc phylogenomics phylogeny sequence-alignment genomic-data-analysis genomics-visualization pathogens nchhstp nchhstp-dhp
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- TypeScript
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
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- C++
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
genomics genome-sequencing genomes oxford-nanopore genome-analysis genome-assembly genomic-data-analysis genome-scale-models human-genetics
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- Python
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
bioinformatics genome taxonomy metagenomics classification fasta fastq metagenomes dna-sequences short-read-mapper read-mapping metagenomic-analysis metagenomic-classification genomic-data-analysis bioinformatics-algorithms long-reads metagenomic-data refseq ncbi-refseq bioinformatics-tool
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- C++
RADseq Data Exploration, Manipulation and Visualization using R
visualization genomics genetics filter outliers imputation missingness gbs normalization radseq radseq-data genomic-data-analysis genotype-likelihoods genomics-visualization genotyping-by-sequencing batch-effects heterozygosity artifacts-detection paralogs outliers-detection
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- HTML
Phigaro is a scalable command-line tool for predicting phages and prophages
bioinformatics genomics bioinformatics-pipeline biological-data-analysis bioinformatics-analysis genomic-data-analysis phage genomic-regions bioinformatics-tool phages prophage
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The AnnSQL package enables SQL based queries on AnnData objects.
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- Python
Shiny app for making and annotating Volcano plots
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- R
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
package benchmarking genomics graph-algorithms genetics gene-expression simulated-data joss simulation-modeling genomic-data-analysis ngs-analysis r-stats gene-regulatory-networks igraph-networks
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(current) 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 snakemake scalable ec2 nextflow ngs slurm budgeting bioinformatics-pipeline informatics scaling cwl wgs ephemeral genomic-data-analysis aws-parallelcluster giab aws-parallel-cluster sarek
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- Python
Genome Contact Map Explorer - gcMapExplorer. Visit:
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- Python
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
visualization bioinformatics deep-learning genomics tabular-data single-cell biomarker-discovery classification-algorithm biomarkers bioinfomatics-pipeline genomic-data-analysis genomics-visualization regression-algorithms data-classification bioinformatics-tool trajectory-inference cell-annotation multi-omic-integration
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- Python
Differential Privacy Protection against MembershipInference Attack on Machine Learning for Genomic Data
machine-learning differential-privacy genomic-data-analysis membership-inference-attack genetic-privacy
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- Python
genomic alignment similarity search tool
fasta sequence-alignments align-dna-sequences dna-sequences sequence-alignment fasta-sequences blastn genomic-data-analysis blast-search spaced-seed
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Collection of statistical scripts, image analysis workflows, data used in publications by the Misteli Lab.
learning workflow r knime cancer biology tensorflow keras deep biological-data-analysis image-analysis genomic-data-analysis misteli-lab
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The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics genomics network-graph phylogenetic-trees phylogenetics epidemiology network-visualization network-analysis hiv cdc phylogenomics phylogeny sequence-alignment genomic-data-analysis genomics-visualization pathogens
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- HTML
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