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Trackplot: A flexible toolkit for combinatorial analysis of genomic data

Here, we introduce Trackplot, a Python package for generating publication-quality visualization by a programmable and interactive web-based approach. Compared to the existing versions of programs generating sashimi plots, Trackplot offers a versatile platform for visually interpreting genomic data f...

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Detalles Bibliográficos
Autores principales: Zhang, Yiming, Zhou, Ran, Liu, Lunxu, Chen, Lu, Wang, Yuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503704/
https://www.ncbi.nlm.nih.gov/pubmed/37669275
http://dx.doi.org/10.1371/journal.pcbi.1011477
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author Zhang, Yiming
Zhou, Ran
Liu, Lunxu
Chen, Lu
Wang, Yuan
author_facet Zhang, Yiming
Zhou, Ran
Liu, Lunxu
Chen, Lu
Wang, Yuan
author_sort Zhang, Yiming
collection PubMed
description Here, we introduce Trackplot, a Python package for generating publication-quality visualization by a programmable and interactive web-based approach. Compared to the existing versions of programs generating sashimi plots, Trackplot offers a versatile platform for visually interpreting genomic data from a wide variety of sources, including gene annotation with functional domain mapping, isoform expression, isoform structures identified by scRNA-seq and long-read sequencing, as well as chromatin accessibility and architecture without any preprocessing, and also offers a broad degree of flexibility for formats of output files that satisfy the requirements of major journals. The Trackplot package is an open-source software which is freely available on Bioconda (https://anaconda.org/bioconda/trackplot), Docker (https://hub.docker.com/r/ygidtu/trackplot), PyPI (https://pypi.org/project/trackplot/) and GitHub (https://github.com/ygidtu/trackplot), and a built-in web server for local deployment is also provided.
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spelling pubmed-105037042023-09-16 Trackplot: A flexible toolkit for combinatorial analysis of genomic data Zhang, Yiming Zhou, Ran Liu, Lunxu Chen, Lu Wang, Yuan PLoS Comput Biol Software Here, we introduce Trackplot, a Python package for generating publication-quality visualization by a programmable and interactive web-based approach. Compared to the existing versions of programs generating sashimi plots, Trackplot offers a versatile platform for visually interpreting genomic data from a wide variety of sources, including gene annotation with functional domain mapping, isoform expression, isoform structures identified by scRNA-seq and long-read sequencing, as well as chromatin accessibility and architecture without any preprocessing, and also offers a broad degree of flexibility for formats of output files that satisfy the requirements of major journals. The Trackplot package is an open-source software which is freely available on Bioconda (https://anaconda.org/bioconda/trackplot), Docker (https://hub.docker.com/r/ygidtu/trackplot), PyPI (https://pypi.org/project/trackplot/) and GitHub (https://github.com/ygidtu/trackplot), and a built-in web server for local deployment is also provided. Public Library of Science 2023-09-05 /pmc/articles/PMC10503704/ /pubmed/37669275 http://dx.doi.org/10.1371/journal.pcbi.1011477 Text en © 2023 Zhang et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Software
Zhang, Yiming
Zhou, Ran
Liu, Lunxu
Chen, Lu
Wang, Yuan
Trackplot: A flexible toolkit for combinatorial analysis of genomic data
title Trackplot: A flexible toolkit for combinatorial analysis of genomic data
title_full Trackplot: A flexible toolkit for combinatorial analysis of genomic data
title_fullStr Trackplot: A flexible toolkit for combinatorial analysis of genomic data
title_full_unstemmed Trackplot: A flexible toolkit for combinatorial analysis of genomic data
title_short Trackplot: A flexible toolkit for combinatorial analysis of genomic data
title_sort trackplot: a flexible toolkit for combinatorial analysis of genomic data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503704/
https://www.ncbi.nlm.nih.gov/pubmed/37669275
http://dx.doi.org/10.1371/journal.pcbi.1011477
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