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Search results for python genomics

372 search results found

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

Deepvariant ⭐ 2,978

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

Pymatgen ⭐ 1,254

Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.

Galaxy ⭐ 1,211

Data intensive science for everyone.

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Cloud-native genomic dataframes and batch computing

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

Goatools ⭐ 673

Python library to handle Gene Ontology (GO) terms

Python library to facilitate genome assembly, annotation, and comparative genomics

Deeptools ⭐ 644

Tools to process and analyze deep sequencing data.

A high-performance, Pythonic language for bioinformatics

Orthofinder ⭐ 547

Phylogenetic orthology inference for comparative genomics

Pycirclize ⭐ 476

Circular visualization in Python (Circos Plot, Chord Diagram)

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

Pyranges ⭐ 371

Performant Pythonic GenomicRanges

Enformer Pytorch ⭐ 359

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Arvados ⭐ 354

An open source platform for managing and analyzing biomedical big data

Nucleotide Transformer ⭐ 305

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

Canvasxpress ⭐ 282

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Genometools ⭐ 261

GenomeTools genome analysis system.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Intermine ⭐ 228

A powerful open source data warehouse system

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Kipoi's model zoo API

Ga4gh Schemas ⭐ 213

Models and APIs for Genomic data. RETIRED 2018-01-24

Hicexplorer ⭐ 197

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Circlator ⭐ 193

A tool to circularize genome assemblies

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

A cool place to store your Hi-C

Pygenomeviz ⭐ 177

A genome visualization python package for comparative genomics

Aiogoogle ⭐ 165

Async Google API Client + Async Google Auth

Msprime ⭐ 161

Simulate genealogical trees and genomic sequence data using population genetic models

web-based analysis tool for rare disease genomics

Readfish ⭐ 152

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Model zoo for genomics

Gatk Sv ⭐ 148

A structural variation pipeline for short-read sequencing

Antimicrobial Resistance Identification By Assembly

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Gubbins ⭐ 133

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Population-scale genomics

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

Neusomatic ⭐ 124

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

Identification of differential RNA modifications from nanopore direct RNA sequencing

Igv Snapshot Automator ⭐ 122

Script to automatically create and run IGV snapshot batchscripts

Redundans ⭐ 121

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

Open Cravat ⭐ 98

A modular annotation tool for genomic variants

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Ga4gh Server ⭐ 95

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Earlgrey ⭐ 90

Earl Grey: A fully automated TE curation and annotation pipeline

mgatk: mitochondrial genome analysis toolkit

Hgtector ⭐ 87

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Gnomad_methods ⭐ 80

Hail helper functions for the gnomAD project and Translational Genomics Group

Tiledb Vcf ⭐ 79

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Comparative Genomics Toolkit 3

Bayesian genotyper for structural variants

Genomics ⭐ 78

Scripts, utilities and programs for genomic bioinformatics.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Python package and CLI for whole-genome duplication related analyses

Pan-genome wide association studies

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

Amazon Web Services Operator Interface

Coolpuppy ⭐ 66

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Merging, Annotation, Validation, and Illustration of Structural variants

Dna Traits ⭐ 64

A fast 23andMe genome text file parser, now superseded by arv

A package for designing compact and comprehensive capture probe sets.

Phanotate ⭐ 58

PHANOTATE: a tool to annotate phage genomes.

A fast, scalable, and accurate local ancestry method.

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

Simplesam ⭐ 55

Simple pure Python SAM parser and objects for working with SAM records

Stacks_workflow ⭐ 54

RADseq workflow built around STACKS

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Trackplot ⭐ 52

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.

Genomegtftools ⭐ 52

convert various features into a GFF-like file for use in genome browsers

Geneview ⭐ 51

Genomics data visualization in Python by using matplotlib.

Mustache ⭐ 50

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Flash Genomics Model ⭐ 49

My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other hierarchical methods)

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Predict AMPs in (meta)genomes and peptides

Full_spectrum_bioinformatics ⭐ 47

An open-access bioinformatics text

Learn interpretable computational phenotyping models from k-merized genomic data

C.origami ⭐ 47

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

Pipelines Api Examples ⭐ 46

Examples for the Google Genomics Pipelines API.

Chromosight ⭐ 46

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Deep Neural Networks Healthcare ⭐ 46

Tangible and Practical Deep Learning Projects Repository for Healthcare such as Cancer, Drug Discovery, Genomic and More

Pymatgen Db ⭐ 46

Pymatgen-db provides an addon to the Python Materials Genomics (pymatgen) library (https://pypi.python.org/pypi/pymatgen) that allows the creation of Materials Project-style databases for management of materials data.

GEne Cluster prediction with COnditional random fields.

Python3 scripts to manipulate FASTA and FASTQ files

Vrs Python ⭐ 44

GA4GH Variation Representation Python Implementation

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Neural Admixture ⭐ 44

Rapid population clustering with autoencoders

Sevenbridges Python ⭐ 44

SevenBridges Python Api bindings

Quota Alignment ⭐ 44

Guided synteny alignment between duplicated genomes (within specified quota constraint)

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

Elucidating the Utility of Genomic Elements with Neural Nets

Covid 19 Genomes ⭐ 43

Projects on COVID-19 topic of genomic sequencing - mostly DataViz

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