Topic: genomics Goto Github

👇 Here are 2377 public repositories matching this topic...

aidenlab / juicer
genomics,A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Organization: aidenlab
Home Page: http://aidenlab.org
3d-genome 3d-genome-browser genomics hi-c bioinformatics ngs

arvados / arvados
genomics,An open source platform for managing and analyzing biomedical big data
Organization: arvados
Home Page: https://arvados.org
arvados ruby python go docker cluster cloud cwl bigdata bioinformatics

benlangmead / bowtie2
genomics,A fast and sensitive gapped read aligner
User: benlangmead
bioinformatics read-aligners genomics c-plus-plus

bigdatagenomics / adam
genomics,ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Organization: bigdatagenomics
spark big-data bioinformatics genomics parquet avro scala java python r

biojava / biojava
genomics,:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Organization: biojava
Home Page: https://biojava.org
bioinformatics java protein-structure genomics protein-sequences protein-modification sequence-alignment structure-alignment protein-data-bank pdb

biopython / biopython
genomics,Official git repository for Biopython (originally converted from CVS)
Organization: biopython
Home Page: http://biopython.org/
python bioinformatics genomics biopython protein protein-structure sequence-alignment phylogenetics dna

brentp / cyvcf2
genomics,cython + htslib == fast VCF and BCF processing
User: brentp
vcf htslib cython genomics bioinformatics

brentp / vcfanno
genomics,annotate a VCF with other VCFs/BEDs/tabixed files
User: brentp
Home Page: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
bioinformatics vcf annotation genomics

broadinstitute / gatk
genomics,Official code repository for GATK versions 4 and up
Organization: broadinstitute
Home Page: https://software.broadinstitute.org/gatk
genomics spark science dna ngs sequencing genome bioinformatics gatk

bwa-mem2 / bwa-mem2
genomics,The next version of bwa-mem
Organization: bwa-mem2
bioinformatics genomics sequence-alignment

chhylp123 / hifiasm
genomics,Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
User: chhylp123
bioinformatics denovo-assembly genomics hifi-read pacbio

deeptools / deeptools
genomics,Tools to process and analyze deep sequencing data.
Organization: deeptools
python bioinformatics genomics ngs rna-seq chip-seq

eggnogdb / eggnog-mapper
genomics,Fast genome-wide functional annotation through orthology assignment
Organization: eggnogdb
Home Page: http://eggnog-mapper.embl.de
annotations orthology-assignments functional-annotation genomics

flowhub-team / awesome-omics
genomics,A collection of awesome things regarding all omics.
User: flowhub-team
genomics protein single-cell ngs ngs-pipeline wgs-analysis awesome omics

fulcrumgenomics / fgbio
genomics,Tools for working with genomic and high throughput sequencing data.
Organization: fulcrumgenomics
Home Page: http://fulcrumgenomics.github.io/fgbio/
analyzing-genomic-data umi bioinformatics ngs scala fgbio molecular-indexes genomics

galaxyproject / galaxy
genomics,Data intensive science for everyone.
Organization: galaxyproject
Home Page: https://galaxyproject.org
bioinformatics workflow genomics science sequencing ngs dna usegalaxy pipeline workflow-engine

gmod / jbrowse
genomics,JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
Organization: gmod
Home Page: http://jbrowse.org
genomics genome-browser genome-annotation protein-annotation bioinformatics biology

google / deepvariant
genomics,DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Organization: google
tensorflow deep-neural-network genomics science dna sequencing genome bioinformatics deep-learning ngs

google / nucleus
genomics,Python and C++ code for reading and writing genomics data.
Organization: google
genomics tensorflow dna bioinformatics

greenelab / deep-review
genomics,A collaboratively written review paper on deep learning, genomics, and precision medicine
Organization: greenelab
Home Page: https://greenelab.github.io/deep-review/
deep-learning neural-networks review genomics manuscript manubot

hail-is / hail
genomics,Cloud-native genomic dataframes and batch computing
Organization: hail-is
Home Page: https://hail.is
genetics vcf genomics gwas bioinformatics python software hail

hazyresearch / hyena-dna
genomics,Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
Organization: hazyresearch
Home Page: https://arxiv.org/abs/2306.15794
foundation-models genomics language-models

higlass / higlass
genomics,Fast, flexible and extensible genome browser.
Organization: higlass
Home Page: http://higlass.io
genomics visualization higlass hi-c gehlenborglab

illumina / hap.py
genomics,Haplotype VCF comparison tools
Organization: illumina
vcf-comparison vcf bioinformatics genomics

instadeepai / nucleotide-transformer
genomics,🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Organization: instadeepai
Home Page: https://www.biorxiv.org/content/10.1101/2023.01.11.523679v2
genomics deep-learning language-model nucleotide transformer dna

j-andrews7 / awesome-bioinformatics-benchmarks
genomics,A curated list of bioinformatics bench-marking papers and resources.
User: j-andrews7
collection bioinformatics-benchmarks benchmarking-study genomics bioinformatics

kblin / ncbi-genome-download
genomics,Scripts to download genomes from the NCBI FTP servers
User: kblin
ncbi bioinformatics download-genomes python biology genomics command-line genbank

lh3 / bwa
genomics,Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
User: lh3
bioinformatics sequence-alignment genomics fm-index

lh3 / minigraph
genomics,Sequence-to-graph mapper and graph generator
User: lh3
Home Page: https://lh3.github.io/minigraph
bioinformatics genomics sequence-alignment genome-graph pan-genome

lh3 / minimap2
genomics,A versatile pairwise aligner for genomic and spliced nucleotide sequences
User: lh3
Home Page: https://lh3.github.io/minimap2
bioinformatics sequence-alignment spliced-alignment genomics

lindenb / jvarkit
genomics,Java utilities for Bioinformatics
User: lindenb
Home Page: https://jvarkit.readthedocs.io/
bioinformatics java next-generation-sequencing ngs science biology genomics

lucidrains / enformer-pytorch
genomics,Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
User: lucidrains
artificial-intelligence deep-learning gene-expression attention-mechanism transformer dna-sequences genomics

luntergroup / octopus
genomics,Bayesian haplotype-based mutation calling
Organization: luntergroup
genomics variant-calling bioinformatics variants haplotypes somatic-variants de-novo-mutation phasing single-cell

mareesat / gwa_tutorial
genomics,A comprehensive tutorial about GWAS and PRS
User: mareesat
gwas qc prs r plink genetics population-structure unix population-stratification genomics

mdshw5 / pyfaidx
genomics,Efficient pythonic random access to fasta subsequences
User: mdshw5
Home Page: https://pypi.python.org/pypi/pyfaidx
python bioinformatics fasta indexing dna protein genomics bgzf samtools

moshi4 / pycirclize
genomics,Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
User: moshi4
Home Page: https://moshi4.github.io/pyCirclize/
bioinformatics circos matplotlib python chord-diagram comparative-genomics genomics genomics-visualization microbial-genomics visualization

nanoporetech / dorado
genomics,Oxford Nanopore's Basecaller
Organization: nanoporetech
Home Page: https://nanoporetech.com/
basecalling libtorch nanopore genomics

nf-core / sarek
genomics,Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Organization: nf-core
Home Page: https://nf-co.re/sarek
nextflow workflow pipeline bioinformatics genomics cancer next-generation-sequencing conda reproducible-research containers

pinellolab / dna-diffusion
genomics,🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
Organization: pinellolab
Home Page: https://pinellolab.github.io/DNA-Diffusion/
deep-learning diffusion-models genomics regulatory-genomics stable-diffusion generative-model diffusion-probabilistic-models

poisonalien / maftools
genomics,Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
User: poisonalien
Home Page: http://bioconductor.org/packages/release/bioc/html/maftools.html
maf-files cancer-genomics cancer-genome-atlas tcga genomics bioinformatics r

priyank-purohit / postgui
genomics,A React web application to query and share any PostgreSQL database.
User: priyank-purohit
reactjs postgresql postgres postgrest gui dashboard bioinformatics genomics data-sharing database

pyranges / pyranges
genomics,Performant Pythonic GenomicRanges
Organization: pyranges
Home Page: https://pyranges.readthedocs.io
genomicranges python genomics pandas data-structures

seq-lang / seq
genomics,A high-performance, Pythonic language for bioinformatics
Organization: seq-lang
Home Page: https://seq-lang.org
bioinformatics computational-biology genomics programming-language domain-specific-language compiler python

tanghaibao / goatools
genomics,Python library to handle Gene Ontology (GO) terms
User: tanghaibao
gene-ontology genomics gene-set-enrichment fdr bioinfomatics goslim-terms fisher-tests fdr-benjamini sidak holm-sidak

tanghaibao / jcvi
genomics,Python library to facilitate genome assembly, annotation, and comparative genomics
User: tanghaibao
genomics genome-sequencing comparative-genomics variant-calling genetic-maps sequence-alignments bioinformatics synteny allmaps assembly

tariqdaouda / pygeno
genomics,Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
User: tariqdaouda
Home Page: http://pygeno.iric.ca
bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

tseemann / snippy
genomics,:scissors: :zap: Rapid haploid variant calling and core genome alignment
User: tseemann
variant-calling haploid bacteria fastq-analysis snps vcf indel-discovery bioinformatics genomics

vcflib / vcflib
genomics, C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Organization: vcflib
Home Page: https://github.com/vcflib/vcflib#vcflib
variant-calling genomics vcf-manipulation genotyping haplotypecaller

vgteam / vg
genomics,tools for working with genome variation graphs
Organization: vgteam
Home Page: https://biostars.org/tag/vg/
variation-graph graph genome-graph genomics dna

voutcn / megahit
genomics,Ultra-fast and memory-efficient (meta-)genome assembler
User: voutcn
Home Page: http://www.ncbi.nlm.nih.gov/pubmed/25609793
bioinformatics metagenomics succinct data-structures genomics genome-assembly