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 375
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 135
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 116
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 89
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
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++ 58
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++ 57
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 50
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
Language:R 29
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
jakublipinski / build-deepsea-training-dataset
Build DeepSea training dataset from raw data
genomic-data-analysis
Language:Python 23
VolcaNoseR
JoachimGoedhart / VolcaNoseR
Shiny app for making and annotating Volcano plots
dataviz genomic-data-analysis ggplot2 proteomics-data-analysis shiny shinyapp volcano
Language:R 22
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 21
rjdkmr / gcMapExplorer
Genome Contact Map Explorer - gcMapExplorer. Visit:
bioinformatics genomic-data-analysis hi-c
Language:Python 21
laurentnoe / yass
genomic alignment similarity search tool
align-dna-sequences blast-search blastn dna-sequences fasta fasta-sequences genomic-data-analysis sequence-alignment sequence-alignments spaced-seed
Language:C 19
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 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 15
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 bioinformatics genome genomic-data-analysis genomic-regions permutation-test randomization rstats
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 11
Poissonfish / iPat
iPat allows you to perform GWAS and GS with drags and clicks!
analysis association-studies gene-prediction genome genome-analysis genomic-data-analysis genomics gui gwas hapmap ipat vcf
Language:Java 11
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
bam-files c cram-files fastq-files genomic-data-analysis htslib sam sam-files vcf-files
Language:C 10
fjdf / slaMEM
Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array
dna genome-analysis genomic-data-analysis genomics-visualization maximal-exact-matches mem mummer sequencing
Language:C 10
INMEGEN / Pipelines_INMEGEN
Flujos de trabajos desarrollados y automatizados en el Inmegen para el procesamiento de datos genómicos y transcriptómicos.
bioinformatics rnaseq-analysis somatic-variants variant-calling dockerfile genomic-data-analysis nextflow-pipeline transcriptome-analysis
Language:Nextflow 9
CEA-LIST / sgntx
iDASH 2017 competition, track 2 winning team solution
genomic-data-analysis genomics idash intel intel-sgx 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 machine-learning-algorithms workflow
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
mindleaving / genome-tools
Tools for exploration and analysis of biochemical data like genomics and proteins
genomic-data-analysis genomics genomics-visualization molecular-dynamics molecular-simulation molecular-structures molecule pdb pdb-files peptide
Language:C# 6
Sentieon / sentieon-google-genomics
Run Sentieon pipelines on Google Cloud Platform
sentieon gcp cloud-computing bioinformatics-pipeline ngs-pipeline genomic-data-analysis germline-variants somatic-variants speedup
Language:Shell 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 5