bioconductor - PMC

Yahui Zhao, Yang Li, Rui Zhu, Riyue Feng, Heyang Cui, Xiao Yu, Furong Huang, Ruixiang Zhang, Xiankai Chen, Lei Li, Yinghui Chen, Yuhao Liu, Jinhua Wang, Guanhua Du, Zhihua Liu

Signal Transduct Target Ther. 2023; 8: 224. Published online 2023 Jun 2. doi: 10.1038/s41392-023-01428-1

PMCID:: PMC10235050

Article PubReader PDF–6.3M Cite

Select item 101877054.

An Integrative Multi-Omics Analysis of The Molecular Links between Aging and Aggressiveness in Thyroid Cancers

Emmanuelle Ruiz, Emad Kandil, Solomon Alhassan, Eman Toraih, Youssef Errami, Zakaria Y. Abd Elmageed, Mourad Zerfaoui

Aging Dis. 2023 Jun 1; 14(3): 992–1012. Published online 2023 Jun 1. doi: 10.14336/AD.2022.1021

PMCID:: PMC10187705

Article PubReader PDF–1.9M Cite

Select item 102350995.

Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Zhou Hong, Dan Peng, Luke R. Tembrock, Xuezhu Liao, Daping Xu, Xiaojing Liu, Zhiqiang Wu

Commun Biol. 2023; 6: 587. Published online 2023 Jun 1. doi: 10.1038/s42003-023-04980-2

PMCID:: PMC10235099

Article PubReader PDF–4.7M Cite

Select item 102368326.

mutscan—a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data

Charlotte Soneson, Alexandra M. Bendel, Guillaume Diss, Michael B. Stadler

Genome Biol. 2023; 24: 132. Published online 2023 Jun 1. doi: 10.1186/s13059-023-02967-0

PMCID:: PMC10236832

Article PubReader PDF–4.0M Cite

Select item 102320077.

Silencing miR-21-5p in sensory neurons reverses neuropathic allodynia via activation of TGF-β–related pathway in macrophages

Lynda Zeboudj, George Sideris-Lampretsas, Rita Silva, Sabeha Al-Mudaris, Francesca Picco, Sarah Fox, David Chambers, Marzia Malcangio

J Clin Invest. 2023 Jun 1; 133(11): e164472. Published online 2023 Jun 1. doi: 10.1172/JCI164472

PMCID:: PMC10232007

Article PubReader PDF–12M Cite

Select item 102338868.

CrypticProteinDB: an integrated database of proteome and immunopeptidome derived non-canonical cancer proteins

Ghofran Othoum, Christopher A Maher

NAR Cancer. 2023 Jun; 5(2): zcad024. Published online 2023 Jun 1. doi: 10.1093/narcan/zcad024

PMCID:: PMC10233886

Article PubReader PDF–2.1M Cite

Select item 102351339.

Transposon signatures of allopolyploid genome evolution

Adam M. Session, Daniel S. Rokhsar

Nat Commun. 2023; 14: 3180. Published online 2023 Jun 1. doi: 10.1038/s41467-023-38560-z

PMCID:: PMC10235133

Article PubReader PDF–3.0M Cite

Select item 1023425110.

Ageing restructures the transcriptome of the hypothalamic supraoptic nucleus and alters the response to dehydration

Ghadir Elsamad, André Souza Mecawi, Audrys G. Pauža, Benjamin Gillard, Alex Paterson, Victor J. Duque, Olivera Šarenac, Nina Japundžić Žigon, Mingkwan Greenwood, Michael P. Greenwood, David Murphy

NPJ Aging. 2023 Dec; 9(1): 12. Published online 2023 Jun 1. doi: 10.1038/s41514-023-00108-2

PMCID:: PMC10234251

Article PubReader PDF–4.2M Cite

Select item 1023508911.

Deep computational image analysis of immune cell niches reveals treatment-specific outcome associations in lung cancer

Cristian Barrera, Germán Corredor, Vidya Sankar Viswanathan, Ruiwen Ding, Paula Toro, Pingfu Fu, Christina Buzzy, Cheng Lu, Priya Velu, Philipp Zens, Sabina Berezowska, Merzu Belete, David Balli, Han Chang, Vipul Baxi, Konstantinos Syrigos, David L. Rimm, Vamsidhar Velcheti, Kurt Schalper, Eduardo Romero, Anant Madabhushi

NPJ Precis Oncol. 2023; 7: 52. Published online 2023 Jun 1. doi: 10.1038/s41698-023-00403-x

PMCID:: PMC10235089

Article PubReader PDF–9.5M Cite

Select item 1018767412.

clipplotr—a comparative visualization and analysis tool for CLIP data

Anob M. Chakrabarti, Charlotte Capitanchik, Jernej Ule, Nicholas M. Luscombe

RNA. 2023 Jun; 29(6): 715–723. doi: 10.1261/rna.079326.122

PMCID:: PMC10187674

Article PubReader PDF–2.8M Cite

Select item 1023424513.

Epigenomic landscape exhibits interferon signaling suppression in the patient of myocarditis after BNT162b2 vaccination

Hyeonhui Kim, Hyo-Suk Ahn, Nahee Hwang, Yune Huh, Seonghyeon Bu, Kyung Jin Seo, Se Hwan Kwon, Hae-Kyung Lee, Jae-woo Kim, Bo Kyung Yoon, Sungsoon Fang

Sci Rep. 2023; 13: 8926. Published online 2023 Jun 1. doi: 10.1038/s41598-023-36070-y

PMCID:: PMC10234245

Article PubReader PDF–6.2M Cite

Select item 1023013314.

Teaching Academic Staff to Implement Interactive Graphics for Their Courses

Pamela Liebig, Viviane Filor, Mariana Scheumann, Martina Buchholz, Klaus Jung

Tech Know Learn. 2023 May 31 : 1–22. doi: 10.1007/s10758-023-09652-y [Epub ahead of print]

PMCID:: PMC10230133

Abstract Article PDF–1.1M Cite

Select item 1023078415.

Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing

Danh D. Truong, Salah-Eddine Lamhamedi-Cherradi, Robert W. Porter, Sandhya Krishnan, Jyothishmathi Swaminathan, Amber Gibson, Alexander J. Lazar, J. Andrew Livingston, Vidya Gopalakrishnan, Nancy Gordon, Najat C. Daw, Nicholas E. Navin, Richard Gorlick, Joseph A. Ludwig

BMC Cancer. 2023; 23: 488. Published online 2023 May 31. doi: 10.1186/s12885-023-10977-1

PMCID:: PMC10230784

Article PubReader PDF–2.5M Cite

Select item 1023070816.

Lactate metabolism-related genes to predict the clinical outcome and molecular characteristics of endometrial cancer

Rui Shi, Haojia Li, Sitian Wei, Zhicheng Yu, Jun Zhang, Qi Zhang, Ting Zhou, Yuwei Yao, Qian Zhang, Tangansu Zhang, Hongbo Wang

BMC Cancer. 2023; 23: 491. Published online 2023 May 31. doi: 10.1186/s12885-023-10934-y

PMCID:: PMC10230708

Article PubReader PDF–8.8M Cite

Select item 1023077917.

A risk signature of ubiquitin-specific protease family predict the prognosis and therapy of kidney cancer patients

Renjie Wang, Yang Liu, Jingxian Li, Yubao Zhao, Rui An, Zhifang Ma

BMC Nephrol. 2023; 24: 153. Published online 2023 May 31. doi: 10.1186/s12882-023-03215-0

PMCID:: PMC10230779

Article PubReader PDF–7.9M Cite

Select item 1023331218.

Znf469 Plays a Critical Role in Regulating Synthesis of ECM: A Zebrafish Model of Brittle Cornea Syndrome

Jing Bao, Xiaoning Yu, Xiyuan Ping, Xingchao Shentu, Jian Zou

Invest Ophthalmol Vis Sci. 2023 May; 64(5): 29. Published online 2023 May 31. doi: 10.1167/iovs.64.5.29

PMCID:: PMC10233312

Article PubReader PDF–3.3M Cite

Select item 1023249019.

Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

Marjan M. Naeini, Felicity Newell, Lauren G. Aoude, Vanessa F. Bonazzi, Kalpana Patel, Guy Lampe, Lambros T. Koufariotis, Vanessa Lakis, Venkateswar Addala, Olga Kondrashova, Rebecca L. Johnston, Sowmya Sharma, Sandra Brosda, Oliver Holmes, Conrad Leonard, Scott Wood, Qinying Xu, Janine Thomas, Euan Walpole, G. Tao Mai, Stephen P. Ackland, Jarad Martin, Matthew Burge, Robert Finch, Christos S. Karapetis, Jenny Shannon, Louise Nott, Robert Bohmer, Kate Wilson, Elizabeth Barnes, John R. Zalcberg, B. Mark Smithers, John Simes, Timothy Price, Val Gebski, Katia Nones, David I. Watson, John V. Pearson, Andrew P. Barbour, Nicola Waddell

Nat Commun. 2023; 14: 3155. Published online 2023 May 31. doi: 10.1038/s41467-023-38891-x

PMCID:: PMC10232490

Article PubReader PDF–4.7M Cite

Select item 1022959220.

Learning perturbation-inducible cell states from observability analysis of transcriptome dynamics

Aqib Hasnain, Shara Balakrishnan, Dennis M. Joshy, Jen Smith, Steven B. Haase, Enoch Yeung

Nat Commun. 2023; 14: 3148. Published online 2023 May 31. doi: 10.1038/s41467-023-37897-9

PMCID:: PMC10229592

Article PubReader PDF–2.6M Cite

<< First< Prev

Page of 3433

Next >Last >>

Supplemental Content

Filter your results:

Manage Filters

PMC Images search for bioconductor

Figure 3:Bioconductor workflow for analyzing single-cell data.

A typical analytical workflow using Bioconductor leads to the creation and evolution of a SingleCellExperiment (or sce) object during data processing and downstream statistical analysis (left column). An example of a sce object evolving throughout the course of a workflow is shown, including visualization, analysis, and annotation (right column).

Orchestrating Single-Cell Analysis with Bioconductor

Nat Methods. ;17(2):137-145.
Figure 1:Number of Bioconductor packages for the analysis of high-throughput sequencing data over ten years.

Bioconductor software packages associated with the analysis of sequencing data were tracked by date of submission over the course of ten years. Software packages were uniquely defined by their primary sequencing technology association, with examples of specific terms used for annotation in parentheses.

Orchestrating Single-Cell Analysis with Bioconductor

Nat Methods. ;17(2):137-145.
Figure 1

Implementing a Bioconductor class in Python. Implementing a Bioconductor class can be performed by either declaring all class components explicitly (right), or by relying on meta-programming utilities found in the rpy2 package (left). Meta-programming helps reduce the amount of boilerplate code by automating part of the translation work.

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators

BMC Bioinformatics. 2010;11(Suppl 12):S11-S11.
Figure 2

Heat map (produced by the Bioconductor function heatmap()) of the ALL leukemia data.

Bioconductor: open software development for computational biology and bioinformatics

Genome Biol. 2004;5(10):R80-R80.