cobilab/jarvis3

Efficient compression of biological data

Language: C - Size: 75.6 MB - Last synced: about 10 hours ago - Pushed: about 11 hours ago - Stars: 3 - Forks: 0

broadinstitute/gatk

Official code repository for GATK versions 4 and up

Language: Java - Size: 453 MB - Last synced: about 10 hours ago - Pushed: about 12 hours ago - Stars: 1,611 - Forks: 574

ratschlab/metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

Language: C++ - Size: 73.3 MB - Last synced: about 14 hours ago - Pushed: about 14 hours ago - Stars: 90 - Forks: 14

nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Language: TypeScript - Size: 57.1 MB - Last synced: about 14 hours ago - Pushed: about 14 hours ago - Stars: 200 - Forks: 57

anton083/VectorizedKmers.jl

Fast K-mer counting in Julia

Language: Julia - Size: 719 KB - Last synced: about 17 hours ago - Pushed: about 19 hours ago - Stars: 9 - Forks: 0

samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

Language: Java - Size: 155 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 273 - Forks: 244

yugalnshah/Forensic-Analysis

practice using Binary Search Trees to analyze DNA.

Language: Java - Size: 31.3 KB - Last synced: about 20 hours ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

fomightez/sequencework

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Language: Python - Size: 3.58 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 24 - Forks: 4

tzok/eltetrado

A Python application to find and classify tetrads and quadruplexes in DNA/RNA 3D structures

Language: Python - Size: 3.05 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 17 - Forks: 3

liberu-genealogy/php-dna

Language: PHP - Size: 665 KB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 31 - Forks: 23

MAGICS-LAB/DNABERT_S

DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models

Language: Python - Size: 2.72 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 22 - Forks: 7

biopython/biopython

Official git repository for Biopython (originally converted from CVS)

Language: Python - Size: 67.9 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 4,182 - Forks: 1,720

lorenzo-rovigatti/oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings

Language: C++ - Size: 48 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 38 - Forks: 26

BjornFJohansson/pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

Language: Jupyter Notebook - Size: 47.6 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 155 - Forks: 40

iliapopov17/The-shadow-of-HIV

Repository for course project in Bioinformatics Institute 2023-2024

Language: Jupyter Notebook - Size: 30 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 1

cgohlke/dnacurve

DNA curvature analysis

Language: Python - Size: 157 KB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 5 - Forks: 1

CiaranOMara/BedgraphFiles.jl

FileIO.jl integration for bedGraph files

Language: Julia - Size: 104 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 2 - Forks: 6

nf-core/hlatyping

Precision HLA typing from next-generation sequencing data

Language: Nextflow - Size: 39.3 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 52 - Forks: 28

nf-core/circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

Language: Python - Size: 184 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 25 - Forks: 14

arms-mbon/data_workspace

This repo is the working area for ARMS-MBON event and omics data: data are collected, harvested, combined, reformatted

Language: Python - Size: 39.3 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 2 - Forks: 1

paulsengroup/modle

High-performance stochastic modeling of DNA loop extrusion interactions

Language: C++ - Size: 67.9 MB - Last synced: 9 days ago - Pushed: 11 days ago - Stars: 16 - Forks: 1

camilogarciabotero/BioMarkovChains.jl

Representing biological sequences as Markov chains

Language: Julia - Size: 3.19 MB - Last synced: 9 days ago - Pushed: 11 days ago - Stars: 7 - Forks: 2

apriha/snps

tools for reading, writing, merging, and remapping SNPs

Language: Python - Size: 2.06 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 91 - Forks: 18

CiaranOMara/Bedgraph.jl

Read and write support for bedGraph file format.

Language: Julia - Size: 126 KB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 5

Fraternalilab/POPScomp

Solvent Accessible Surface Areas of Biomolecules and their Complexes

Language: C - Size: 5.97 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 14 - Forks: 3

spawaskar-cora/cora-docs

CoRA Docs

Language: HTML - Size: 569 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 36 - Forks: 5

Aavache/awesome-genetic-ai-papers

Recent awesome AI papers about genomics.

Size: 9.77 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

Jumitti/TFinder

Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.

Language: Python - Size: 60.6 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 6 - Forks: 10

Arty40m/nskit

RNA/DNA secondary structure library for processing it as a graph, reading and writing

Language: Python - Size: 178 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 3 - Forks: 1

bebop/poly

A Go package for engineering organisms.

Language: Go - Size: 12.9 MB - Last synced: about 1 hour ago - Pushed: 17 days ago - Stars: 653 - Forks: 68

novoalab/modPhred

modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

Language: Python - Size: 47.9 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 13 - Forks: 1

MichaelSebero/GEDmatch-Admixture-Sorter

This python script sorts a population spreadsheet provided by GEDmatch.

Language: Python - Size: 24.4 KB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 0 - Forks: 0

marrink-lab/polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

Language: Python - Size: 7.33 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 110 - Forks: 20

mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

Language: Python - Size: 11.7 MB - Last synced: 6 days ago - Pushed: 22 days ago - Stars: 441 - Forks: 73

yaoguangluo/ChromosomeDNA

《DNA元基催化与肽计算》 在进化计算中, 软件函数文件进行 DNA 语义元基索引编码的 PDE 新陈代谢优化方式, 是一种有效的进化方式.

Language: Java - Size: 670 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 7 - Forks: 2

galaxyproject/galaxy

Data intensive science for everyone.

Language: Python - Size: 616 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 1,315 - Forks: 961

Lattice-Automation/primers

A PCR primer tool for DNA assembly flows

Language: Python - Size: 70.3 KB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 22 - Forks: 6

mutalyzer/algebra

A Boolean Algebra for Genetic Variants

Language: Python - Size: 854 KB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 10 - Forks: 2

Gulshan-gaur/NAUniSeq

NAUniSeq: A fast computational pipeline to search unique sequences for microbial diagnostics

Language: Python - Size: 853 KB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 1 - Forks: 0

ropensci/restez

:sleeping: :open_file_folder: Create and Query a Local Copy of GenBank in R

Language: R - Size: 10 MB - Last synced: 5 days ago - Pushed: 28 days ago - Stars: 25 - Forks: 5

instadeepai/nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Language: Python - Size: 4.05 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 377 - Forks: 45

shyambhakta/wetlabcalc

Wetlab Calculator

Size: 1.52 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 12 - Forks: 0

Dpbm/dna-quantum

RNA to DNA using quantum computing

Language: Jupyter Notebook - Size: 60.5 KB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 0 - Forks: 0

vgteam/vg

tools for working with genome variation graphs

Language: C++ - Size: 138 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1,055 - Forks: 189

igordot/sns

Analysis pipelines for genomic sequencing data

Language: Shell - Size: 497 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 60 - Forks: 27

ugeneunipro/ugene

UGENE is free open-source cross-platform bioinformatics software

Language: C++ - Size: 194 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 196 - Forks: 59

drboothtj/gcskewer

create GC skew plots from DNA sequences in python

Language: HTML - Size: 5.48 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

PacificBiosciences/hifihla

An HLA star-calling tool for PacBio HiFi data types

Size: 61.5 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 15 - Forks: 1

jslfree080/interpack

DNA FASTA encoder for compressing raw sequences into searchable binary format (extract nth subsequence using random access without index file)

Language: Rust - Size: 3.02 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

AstraBert/VirBiCla

A novel ML-based binary classifier to tell viral and non-viral long reads apart in metagenomic samples.

Language: Python - Size: 49.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

Lattice-Automation/seqviz

a JavaScript DNA, RNA, and protein sequence viewer

Language: TypeScript - Size: 112 MB - Last synced: 11 days ago - Pushed: about 1 month ago - Stars: 213 - Forks: 48

timkartar/RNAscape

Geometry faithful 2D RNA visualization

Language: Python - Size: 7.87 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

CoolCat467/Coding-For-Medicine-2020

This is a bunch of programs I created in the 2020 Intermediate Coding For Medicine Course. No Stealing.

Language: Python - Size: 85 KB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

VerisimilitudeX/DNAnalyzer

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Language: Java - Size: 188 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 125 - Forks: 55

Delemangi/DnA-project

Дизајн на алгоритми - проект | Algorithm design - project | 2021/2022

Size: 122 KB - Last synced: 1 day ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

FelixKrueger/Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Language: HTML - Size: 38 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 356 - Forks: 102

FelixErnst/Modstrings

:package: Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides.

Language: R - Size: 681 KB - Last synced: 8 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 1

Paradoxdruid/SWVAnyPeakFinder

GUI application for resolving peak heights in square-wave voltammetry datafiles.

Language: Python - Size: 200 KB - Last synced: 24 days ago - Pushed: about 2 months ago - Stars: 6 - Forks: 2

EricLarG4/OligoR

Software suite for oligonucleotide native MS data treatment

Language: R - Size: 247 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 1

cobilab/geco2

An improved compression tool for DNA sequences

Language: C - Size: 307 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 8 - Forks: 2

JinsenLi/deepDNAshape

A method to predict DNA shape features considering farther flanking region.

Language: Python - Size: 58.5 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 8 - Forks: 0

songlab-cal/gpn

Genomic Pre-trained Network

Language: Jupyter Notebook - Size: 52.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 151 - Forks: 19

statgenlmu/coala

A Framework for Coalescent Simulation in R

Language: R - Size: 1.12 MB - Last synced: 26 days ago - Pushed: about 2 months ago - Stars: 22 - Forks: 4

apriha/lineage

tools for genetic genealogy and the analysis of consumer DNA test results

Language: Python - Size: 1.05 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 140 - Forks: 25

google/deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

Size: 20.5 KB - Last synced: 8 days ago - Pushed: about 2 months ago - Stars: 92 - Forks: 11

google/deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Language: Python - Size: 503 MB - Last synced: 8 days ago - Pushed: about 2 months ago - Stars: 3,084 - Forks: 695

jlchen5/Copy-number-analysis

This shell script is for analysing the DNA copy number via WGS data

Language: Shell - Size: 9.77 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

MykytaPetrenko/MetaReForge-Docs

MetaReforge Documentation

Size: 7.16 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

plashchynski/awesome-genetics

A curated list of awesome personal genomics software, libraries, and educational resources.

Size: 40 KB - Last synced: 29 days ago - Pushed: 2 months ago - Stars: 109 - Forks: 7

Monty/DNA_Match_Manager_Helper

Create sortable spreadsheet from DNA Match Manager output files

Language: Shell - Size: 38.1 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 3 - Forks: 0

meghanmshea/intertidal-eDNA

Data and R code for "Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal" (Shea & Boehm)

Language: HTML - Size: 158 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

BjornFJohansson/seguid_calculator

A gui for calculating seguid checksums for biological sequences

Language: Python - Size: 75 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 6 - Forks: 1

microsoft/BindVAE

Variational Auto Encoders for learning binding signatures of transcription factors

Language: Python - Size: 9.41 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 9 - Forks: 2

cgevans/qslib

QSLib is a package for interacting with Applied Biosystems' QuantStudio qPCR machines, intended for non-qPCR uses, such as DNA computing and molecular programming systems.

Language: Python - Size: 1.12 MB - Last synced: 4 days ago - Pushed: 2 months ago - Stars: 7 - Forks: 0

MichaelSebero/Genetic-Trait-Detector

This python script detects known traits in raw human genetic data.

Language: Python - Size: 79.1 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 31 - Forks: 1

timweh/MEMSA

Multiple sequence alignment tool that builds on the concept of seed-and-extend algorithms

Language: C++ - Size: 154 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

fomightez/blast-binder

Repo for running command line-based BLAST in Jupyter environment provided via Binder.

Language: Jupyter Notebook - Size: 2.06 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 7 - Forks: 5

Akodiat/oxJenga Fork of zoombya/oxJenga

exploring vr and steered md concepts

Language: JavaScript - Size: 18.4 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

sh1rokovs/Scientific_Programming_Python

Unn. Course - Python for science

Language: Jupyter Notebook - Size: 198 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

oxpig/CaLM

Protein language model trained on coding DNA

Language: Python - Size: 73.1 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 12 - Forks: 0

wyink/Barcode-DB

rbcL遺伝子もしくはmatK遺伝子の塩基配列から種同定することを目的としたウェブアプリケーション

Language: PHP - Size: 142 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

lmdu/pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Language: C - Size: 9.37 MB - Last synced: 16 days ago - Pushed: 3 months ago - Stars: 238 - Forks: 19

nkvamaks/oligoshell_calc

Oligonucleotide Calculator

Language: JavaScript - Size: 2.53 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

pg-space/panspace

Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes

Language: Jupyter Notebook - Size: 17.8 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

kloetzl/libdna

♥ Essential Functions for DNA Manipulation

Language: C - Size: 901 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 20 - Forks: 0

ajitsingh98/DNA-Classification-Machine-Learning-Project

Classify DNA sequence into Binary class using different Classification algorithms.

Language: Jupyter Notebook - Size: 84 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 4

Daelamy-Yusuf/DNA-Translation

Language: Python - Size: 20.5 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

thejessicafelts/flashcards

Academic Flashcards

Size: 48.8 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

HenrikBengtsson/aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

Language: R - Size: 4.05 MB - Last synced: 8 days ago - Pushed: 3 months ago - Stars: 10 - Forks: 3

moltinginstar/addgene-api

An unofficial API for Addgene, the open-source plasmid repository.

Language: Python - Size: 32.2 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

dib-lab/khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Language: Python - Size: 50.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 729 - Forks: 313

seguid/seguid-dont-use

SEGUID v2: Development and Discussions

Language: HTML - Size: 1.95 MB - Last synced: 26 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 1

Zhihan1996/DNABERT_2

The official implementation of DNABERT-2.

Language: Shell - Size: 711 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 148 - Forks: 31

Lakshanj98/Distinguish-Sequence-Type_Transcription_Translation

Distinguishes the sequence type. Transcribe the DNA to RNA. Translate the RNA to Protein.

Language: Python - Size: 3.91 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

Molmed/clarity-ext

Extensions for Clarity

Language: Python - Size: 1.01 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 8

ErwanDavidCode/Genetic_Algorithm-3dna

The aim of this Python project is to circularize a plasmid by optimizing the values of a table calculating the plasmid's 3D trajectory. To achieve this, 2 algorithms are used and compared: simulated annealing and genetic algorithm.

Language: Python - Size: 8.07 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

RosettaCommons/PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Language: Jupyter Notebook - Size: 353 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 417 - Forks: 138

wbrickner/genonym 📦

Interspecies protein translator + translation optimizer

Language: JavaScript - Size: 20.5 KB - Last synced: 10 days ago - Pushed: 3 months ago - Stars: 5 - Forks: 1

Lioydiano/Starklag

Starklag - a partial evolution simulator

Language: C++ - Size: 15 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 0

Lina674/Complementary_DNA_Sequence_Transcription_and_Translation

This project outputs the complementary DNA sequence of an original sequence, transcribes a DNA sequence to RNA, and translates the RNA sequence to the corresponding sequence of amino acids by identifying the codons that make up the latter.

Language: C# - Size: 20.5 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0