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708 search results found

Deepvariant ⭐ 2,978

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

Nextstrain build for novel coronavirus SARS-CoV-2

Cloud-native genomic dataframes and batch computing

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

Pygenometracks ⭐ 654

python module to plot beautiful and highly customizable genome browser tracks

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

Ban Vqa ⭐ 527

Bilinear attention networks for visual question answering

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

Dnabert ⭐ 471

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Samplot ⭐ 458

Plot structural variant signals from many BAMs and CRAMs

Pytorch Neat ⭐ 387

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Snakepipes ⭐ 359

Customizable workflows based on snakemake and python for the analysis of NGS data

Genomepy ⭐ 355

genes and genomes at your fingertips

Liftoff ⭐ 335

An accurate GFF3/GTF lift over pipeline

Na12878 ⭐ 321

Data and analysis for NA12878 genome on nanopore

Atac Seq Pipeline ⭐ 290

ENCODE ATAC-seq pipeline

Tools for fast and flexible genome assembly scaffolding and improvement

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Pycircos ⭐ 277

a lightweight db framework for exploring genetic variation.

Trycycler ⭐ 264

A tool for generating consensus long-read assemblies for bacterial genomes

Genometools ⭐ 261

GenomeTools genome analysis system.

Funannotate ⭐ 261

Eukaryotic Genome Annotation Pipeline

Celloracle ⭐ 253

This is the alpha version of the CellOracle package

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

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Crispresso2 ⭐ 233

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

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

PEPPER-Margin-DeepVariant

Pyfastx ⭐ 211

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

Getorganelle ⭐ 209

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

Rapid comparison and dereplication of genomes

Nanosim ⭐ 196

Nanopore sequence read simulator

Circlator ⭐ 193

A tool to circularize genome assemblies

Ppanggolin ⭐ 191

Build a partitioned pangenome graph from microbial genomes

Chip Seq Pipeline2 ⭐ 188

ENCODE ChIP-seq pipeline

Full-Length Alternative Isoform analysis of RNA

Tetranscripts ⭐ 164

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

Insilicoseq ⭐ 158

🚀 A sequencing simulator

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Deepevolve ⭐ 151

Rapid hyperparameter discovery for neural nets using genetic algorithms

Layout2im ⭐ 141

Official PyTorch Implementation of Image Generation from Layout - CVPR 2019

Pysamstats ⭐ 141

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Application and Python module for average nucleotide identity analyses of microbes.

Bx Python ⭐ 138

Tools for manipulating biological data, particularly multiple sequence alignments

Blobtools ⭐ 136

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

Atac_dnase_pipelines ⭐ 135

ATAC-seq and DNase-seq processing pipeline

Chromosome-level scaffolding using multiple references

Sigprofilerextractor ⭐ 132

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Ngs_learning ⭐ 131

生物信息学交流资料

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

Badread ⭐ 124

a long read simulator that can imitate many types of read problems

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.

Tensorflow Neuroevolution ⭐ 119

Neuroevolution Framework for Tensorflow 2.x focusing on modularity and high-performance. Preimplements NEAT, DeepNEAT, CoDeepNEAT

Ampliconarchitect ⭐ 119

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up so

Carveme ⭐ 117

CarveMe: genome-scale metabolic model reconstruction

python access to UCSC genomes database

Px2graph ⭐ 113

Training code for "Pixels to Graphs by Associative Embedding"

Oncokb Annotator ⭐ 112

Annotates variants in MAF with OncoKB annotation.

Pyrodigal ⭐ 111

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

Vcf Kit ⭐ 107

VCF-kit: Assorted utilities for the variant call format

Instrain ⭐ 104

Bioinformatics program inStrain

FunGAP: fungal Genome Annotation Pipeline

Large Scale Vrd.pytorch ⭐ 97

Implementation for the AAAI2019 paper "Large-scale Visual Relationship Understanding"

Phylophlan ⭐ 97

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Sigprofilermatrixgenerator ⭐ 91

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

Osgenome ⭐ 90

An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies

Bioinformatics ⭐ 90

Code inspired by Bioinformatics Algorithms: an Active Learning Approach.

mgatk: mitochondrial genome analysis toolkit

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Hgtector ⭐ 87

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

Hybrid Knowledge Routed Module for Large-scale Object Detection (NerIPS2018)

Pipeline Structural Variation ⭐ 87

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Referenceseeker ⭐ 85

Rapid determination of appropriate reference genomes.

Shortstack ⭐ 84

ShortStack: Comprehensive annotation and quantification of small RNA genes

Python graph database framework for bioinformatics

Parliament2 ⭐ 83

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Pb Assembly ⭐ 81

PacBio Assembly Tool Suite: Reads in ⇨ Assembly out

Gnomad_methods ⭐ 80

Hail helper functions for the gnomAD project and Translational Genomics Group

Pytorch Neat ⭐ 80

A pytorch implementation of the NEAT (NeuroEvolution of Augmenting Topologies) algorithm

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Tools for processing and analyzing structural variants.

Mummer2circos ⭐ 79

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

Nucleoatac ⭐ 78

nucleosome calling using ATAC-seq

A fast 23andMe DNA parser and inferrer for Python

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

Super Mario Neat ⭐ 74

This program evolves an AI using the NEAT algorithm to play Super Mario Bros.

Python package and CLI for whole-genome duplication related analyses

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

Ancestry_pipeline ⭐ 71

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

Dfast_core ⭐ 67

DDBJ Fast Annotation and Submission Tool

Guideseq ⭐ 66

Analysis pipeline for the GUIDE-seq assay.

Progressivecactus ⭐ 66

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

Crisporwebsite ⭐ 64

All source code of the crispor.org website

Dna Traits ⭐ 64

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

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