Cargando…

Pygenomics: manipulating genomic intervals and data files in Python

SUMMARY: We present pygenomics, a Python package for working with genomic intervals and bioinformatic data files. The package implements interval operations, provides both API and CLI, and supports reading and writing data in widely used bioinformatic formats, including BAM, BED, GFF3, and VCF. The...

Descripción completa

Detalles Bibliográficos
Autores principales:	Tamazian, Gaik, Cherkasov, Nikolay, Kanapin, Alexander, Samsonova, Anastasia
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Applications Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246576/ https://www.ncbi.nlm.nih.gov/pubmed/37228014 http://dx.doi.org/10.1093/bioinformatics/btad346

Ejemplares similares

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
por: Dale, Ryan K., et al.
Publicado: (2011)

fqtools: an efficient software suite for modern FASTQ file manipulation
por: Droop, Alastair P.
Publicado: (2016)

FUSTA: leveraging FUSE for manipulation of multiFASTA files at scale
por: Delehelle, Franklin, et al.
Publicado: (2022)

A collection of read depth profiles at structural variant breakpoints
por: Bezdvornykh, Igor, et al.
Publicado: (2023)

Gos: a declarative library for interactive genomics visualization in Python
por: Manz, Trevor, et al.
Publicado: (2023)

Crypt4GH: a file format standard enabling native access to encrypted data
por: Senf, Alexander, et al.
Publicado: (2021)

BUSZ: compressed BUS files
por: Einarsson, Pétur Helgi, et al.
Publicado: (2023)

Manipulation of FASTQ data with Galaxy
por: Blankenberg, Daniel, et al.
Publicado: (2010)

Analysing high-throughput sequencing data in Python with HTSeq 2.0
por: Putri, Givanna H, et al.
Publicado: (2022)

bwtool: a tool for bigWig files
por: Pohl, Andy, et al.
Publicado: (2014)

MSPypeline: a python package for streamlined data analysis of mass spectrometry-based proteomics
por: Heming, Simon, et al.
Publicado: (2022)

FRED 2: an immunoinformatics framework for Python
por: Schubert, Benjamin, et al.
Publicado: (2016)

Logomaker: beautiful sequence logos in Python
por: Tareen, Ammar, et al.
Publicado: (2020)

Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python
por: Lubbock, Alexander L R, et al.
Publicado: (2022)

VoDEx: a Python library for time annotation and management of volumetric functional imaging data
por: Nadtochiy, Anna, et al.
Publicado: (2023)

Insane in the vembrane: filtering and transforming VCF/BCF files
por: Hartmann, Till, et al.
Publicado: (2022)

COSMOS: Python library for massively parallel workflows
por: Gafni, Erik, et al.
Publicado: (2014)

graphkernels: R and Python packages for graph comparison
por: Sugiyama, Mahito, et al.
Publicado: (2018)

The EVcouplings Python framework for coevolutionary sequence analysis
por: Hopf, Thomas A, et al.
Publicado: (2019)

PACKMAN-Molecule: Python toolbox for structural bioinformatics
por: Khade, Pranav M, et al.
Publicado: (2022)

GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions
por: Abraham, Abin, et al.
Publicado: (2023)

Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization
por: Wang, Linhua, et al.
Publicado: (2023)

pyBedGraph: a python package for fast operations on 1D genomic signal tracks
por: Zhang, Henry B, et al.
Publicado: (2020)

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge
por: Voytik, Eugenia, et al.
Publicado: (2021)

genozip: a fast and efficient compression tool for VCF files
por: Lan, Divon, et al.
Publicado: (2020)

I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform
por: Wagholikar, Kavishwar B, et al.
Publicado: (2022)

JBrowse Jupyter: a Python interface to JBrowse 2
por: De Jesus Martinez, Teresa, et al.
Publicado: (2023)

pyGOMoDo: GPCRs modeling and docking with python
por: Ribeiro, Rui P, et al.
Publicado: (2023)

ConKit: a python interface to contact predictions
por: Simkovic, Felix, et al.
Publicado: (2017)

cyvcf2: fast, flexible variant analysis with Python
por: Pedersen, Brent S, et al.
Publicado: (2017)

MEWpy: a computational strain optimization workbench in Python
por: Pereira, Vítor, et al.
Publicado: (2021)

pyrpipe: a Python package for RNA-Seq workflows
por: Singh, Urminder, et al.
Publicado: (2021)

Nezzle: an interactive and programmable visualization of biological networks in Python
por: Lee, Daewon
Publicado: (2022)

SquiggleKit: a toolkit for manipulating nanopore signal data
por: Ferguson, James M, et al.
Publicado: (2019)

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
por: Kiefer, Patrick, et al.
Publicado: (2013)

scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data
por: Faure, Louis, et al.
Publicado: (2022)

GAT: a simulation framework for testing the association of genomic intervals
por: Heger, Andreas, et al.
Publicado: (2013)

dipwmsearch: a Python package for searching di-PWM motifs
por: Mille, Marie, et al.
Publicado: (2023)

GIL: a python package for designing custom indexing primers
por: Mateyko, Nicholas, et al.
Publicado: (2023)

localpdb—a Python package to manage protein structures and their annotations
por: Ludwiczak, Jan, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_m0qtl9tt3rpm96r8pnr40efhng