dna

There are 15 repositories under dna topic.

biopython / biopython
Official git repository for Biopython (originally converted from CVS)
python bioinformatics genomics biopython protein protein-structure sequence-alignment phylogenetics dna
Language:Python 4165
google / deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
bioinformatics deep-learning deep-neural-network deepvariant dna genome genomics machine-learning ngs science sequencing tensorflow
Language:Python 3077
broadinstitute / gatk
Official code repository for GATK versions 4 and up
genomics spark science dna ngs sequencing genome bioinformatics gatk
Language:Java 1601
galaxyproject / galaxy
Data intensive science for everyone.
bioinformatics dna genomics hacktoberfest ngs pipeline science sequencing usegalaxy workflow workflow-engine
Language:Python 1314
vgteam / vg
tools for working with genome variation graphs
dna genome-graph genomics graph variation-graph
Language:C++ 1057
google / nucleus
Python and C++ code for reading and writing genomics data.
bioinformatics dna genomics tensorflow
Language:C++ 774
dib-lab / khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
dna k-mer python bloom-filter count-min-sketch graph-traversal bioinformatics
Language:Python 738
poly
bebop / poly
A Go package for engineering organisms.
synthetic-biology synbio genetic-engineering molecular-biology bioengineering computational-biology bioinformatics dna fasta genbank codon-optimizer sequence-hashing plasmids primer-design dna-barcode dna-barcoding golden-gate mash alignment go
Language:Go 648
dna-3d-engine
pallada-92 / dna-3d-engine
3d engine implementation in DNA code!
3d 3d-engine biology chemical-kinetics chemical-reaction-networks chemical-reactions cube dna in-vitro molecular-biology molecular-programming piperine raymarching real-reactive-programming strand-displacement
543
mdshw5 / pyfaidx
Efficient pythonic random access to fasta subsequences
bgzf bioinformatics dna fasta genomics indexing protein python samtools
Language:Python 440
RosettaCommons / PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
pyrosetta google-colab jupyter-notebook protein-design protein-structure-prediction protein-folding protein-docking dna rna-structure-prediction rosetta
Language:Jupyter Notebook 422
SupportIntelligence / Icewater
16,432 Free Yara rules created by
yara malware-analysis cluster threat dna
Language:YARA 379
instadeepai / nucleotide-transformer
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
deep-learning dna genomics language-model nucleotide transformer
Language:Python 377
FelixKrueger / Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
bioinformatics dna methylation
Language:HTML 356
lightdock
lightdock / lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking artificial-intelligence protein-design proteomics structural-biology structural-bioinformatics bioinformatics bioinformatics-tool chemistry molecular-biology molecular-structures
Language:Python 272
samtools / htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
genomics sequencing dna ngs bam cram sam fasta vcf java-api java
Language:Java 271
chanzuckerberg / shasta
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
assembly de-novo dna long-read nanopore pacbio sequencing
Language:C++ 269
BioJulia / Bio.jl
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
bioinformatics biology genomics dna deprecated biojulia biojulia-packages
Language:Julia 261
lmdu / pyfastx
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
assembly bioinformatics biology dna fasta fastq genome python sequence
Language:C 238
seqviz
Lattice-Automation / seqviz
a JavaScript DNA, RNA, and protein sequence viewer
dna igem synthetic-biology vector plasmid rna biology protein
Language:TypeScript 212
nextstrain / nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
clade clades coronavirus covid covid-19 dna ncov neherlab nextstrain research rna sars-cov-2 science sequences sequencing strain virus covid19 next-generation-sequencing influenza
Language:TypeScript 199
ugene
ugeneunipro / ugene
UGENE is free open-source cross-platform bioinformatics software
ugene bioinformatics ngs dna workflow pipeline science cpp qt5 sequencing cross-platform msa
Language:C++ 197
genomics
igordot / genomics
A collection of scripts and notes related to genomics and bioinformatics
bioinformatics genomics sequencing illumina fasta fastq gtf vcf nanopore dna science workflow fast5
Language:R 188
MAGICS-LAB / DNABERT_2
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
covid dataset dna dna-processing dna-training genome genome-analysis language-model promoter promoter-analysis promoters splice splice-site transcription-factor-binding transcription-factor-binding-site transcription-factors
Language:Shell 171
songlab-cal / gpn
Genomic Pre-trained Network
dna language-model variant-effect-prediction
Language:Jupyter Notebook 160
pydna
BjornFJohansson / pydna
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
bioinformatics biopython python anaconda dna gel jupyter-notebooks biology pydna jupyter-notebook gel-simulation jupyter gibson-assembly cloning-strategies gel-electrophoresis assembly-strategies simulation genbank fasta
Language:Jupyter Notebook 152
AIRI-Institute / GENA_LM
GENA-LM is a transformer masked language model trained on human DNA sequence.
dna genomes language-model t2t
Language:Jupyter Notebook 148
apriha / lineage
tools for genetic genealogy and the analysis of consumer DNA test results
dna genes genetics genealogy snps chromosomes genotype bioinformatics ancestry
Language:Python 143
DNAnalyzer
VerisimilitudeX / DNAnalyzer
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
amino-acid-sequence artificial-intelligence bioinformatics dna dna-sequencing genomics hacktoberfest machine-learning metagenomics protein-sequences regulatory-elements sequencing transcriptomics
Language:Java 123
biologyguy / BuddySuite
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
bioinformatics python phylogenetics dna protein alignment command-line workflow biology
Language:Python 121
cslarsen / arv
A fast 23andMe DNA parser and inferrer for Python
23andme bioinformatics dna genome python snpedia snps
Language:C++ 114
awesome-genetics
plashchynski / awesome-genetics
A curated list of awesome personal genomics software, libraries, and educational resources.
genetics genomics 23andme ancestry geneology bioinformatics dna health snpedia consumer-dna-test
111
polyply_1.0
marrink-lab / polyply_1.0
Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
macromolecules martini polymers md coarse-graining dna carbohydrates atomistic-simulations hacktoberfest
Language:Python 109
dotfiles
nosvagor / dotfiles
🍙 my Personalized Development Environment [PDE]
archlinux eww neovim dotfiles linux kitty pde zsh config firefox dna hyprland glava wayland
Language:Lua 105
google / deepsomatic
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
bioinformatics deep-learning dna genome genomics machine science sequencing somatic-mutations somatic-variants deepsomatic
92
apriha / snps
tools for reading, writing, merging, and remapping SNPs
bioinformatics chromosomes dna snps vcf
Language:Python 90