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PMC Full-Text Search Results

Items: 1 to 20 of 5749

1.
A fast machine learning dataloader for epigenetic tracks from BigWig files
Joren Sebastian Retel, Andreas Poehlmann, Josh Chiou, Andreas Steffen, Djork-Arné Clevert
Bioinformatics. 2024 Jan; 40(1): btad767. Published online 2024 Jan 4. doi: 10.1093/bioinformatics/btad767
PMCID:
PMC10782802
ArticlePDF–1.1M
2.
bwtool: a tool for bigWig files
Andy Pohl, Miguel Beato
Bioinformatics. 2014 Jun 1; 30(11): 1618–1619. Published online 2014 Jan 30. doi: 10.1093/bioinformatics/btu056
PMCID:
PMC4029031
ArticlePDF–118K
3.
BigWig and BigBed: enabling browsing of large distributed datasets
W. J. Kent, A. S. Zweig, G. Barber, A. S. Hinrichs, D. Karolchik
Bioinformatics. 2010 Sep 1; 26(17): 2204–2207. Published online 2010 Jul 17. doi: 10.1093/bioinformatics/btq351
PMCID:
PMC2922891
ArticlePDF–237K
4.
smallWig: parallel compression of RNA-seq WIG files
Zhiying Wang, Tsachy Weissman, Olgica Milenkovic
Bioinformatics. 2016 Jan 15; 32(2): 173–180. Published online 2015 Sep 30. doi: 10.1093/bioinformatics/btv561
PMCID:
PMC6078172
ArticlePDF–576K
5.
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data
Vida Ravanmehr, Minji Kim, Zhiying Wang, Olgica Milenković
Bioinformatics. 2018 Mar 15; 34(6): 911–919. Published online 2017 Oct 26. doi: 10.1093/bioinformatics/btx685
PMCID:
PMC5860022
ArticlePDF–721K
6.
Megadepth: efficient coverage quantification for BigWigs and BAMs
Christopher Wilks, Omar Ahmed, Daniel N Baker, David Zhang, Leonardo Collado-Torres, Ben Langmead
Bioinformatics. 2021 Sep 15; 37(18): 3014–3016. Published online 2021 Mar 8. doi: 10.1093/bioinformatics/btab152
PMCID:
PMC8528031
ArticlePDF–401K
7.
Bigtools: a high-performance BigWig and BigBed library in Rust
Jack D. Huey, Nezar Abdennur
Version 1. bioRxiv. Preprint. 2024 Feb 8. doi: 10.1101/2024.02.06.579187
PMCID:
PMC10871241
ArticlePDF–188K
8.
GsmPlot: a web server to visualize epigenome data in NCBI
Jia Li, Yue Yin, Mutian Zhang, Jie Cui, Zhenhai Zhang, Zhiyong Zhang, Deqiang Sun
BMC Bioinformatics. 2020; 21: 55. Published online 2020 Feb 12. doi: 10.1186/s12859-020-3386-0
PMCID:
PMC7017537
ArticlePDF–1.3M
9.
CrossMap: a versatile tool for coordinate conversion between genome assemblies
Hao Zhao, Zhifu Sun, Jing Wang, Haojie Huang, Jean-Pierre Kocher, Liguo Wang
Bioinformatics. 2014 Apr 1; 30(7): 1006–1007. Published online 2013 Dec 18. doi: 10.1093/bioinformatics/btt730
PMCID:
PMC3967108
ArticlePDF–90K
10.
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
Daniel R. Zerbino, Nathan Johnson, Thomas Juettemann, Steven P. Wilder, Paul Flicek
Bioinformatics. 2014 Apr 1; 30(7): 1008–1009. Published online 2013 Dec 19. doi: 10.1093/bioinformatics/btt737
PMCID:
PMC3967112
ArticlePDF–88K
11.
recount3: summaries and queries for large-scale RNA-seq expression and splicing
Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D. Hansen, Ben Langmead
Genome Biol. 2021; 22: 323. Published online 2021 Nov 29. doi: 10.1186/s13059-021-02533-6
PMCID:
PMC8628444
ArticlePDF–5.2M
12.
Prioritising positively selected variants in whole-genome sequencing data using FineMAV
Fadilla Wahyudi, Farhang Aghakhanian, Sadequr Rahman, Yik-Ying Teo, Michał Szpak, Jasbir Dhaliwal, Qasim Ayub
BMC Bioinformatics. 2021; 22: 604. Published online 2021 Dec 18. doi: 10.1186/s12859-021-04506-9
PMCID:
PMC8684245
ArticlePDF–2.0M
13.
The UCSC Genome Browser database: update 2011
Pauline A. Fujita, Brooke Rhead, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Melissa S. Cline, Mary Goldman, Galt P. Barber, Hiram Clawson, Antonio Coelho, Mark Diekhans, Timothy R. Dreszer, Belinda M. Giardine, Rachel A. Harte, Jennifer Hillman-Jackson, Fan Hsu, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Chin H. Li, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Kayla E. Smith, David Haussler, W. James Kent
Nucleic Acids Res. 2011 Jan; 39(Database issue): D876–D882. Published online 2010 Oct 18. doi: 10.1093/nar/gkq963
PMCID:
PMC3242726
ArticlePDF–1.9M
14.
SpliceWiz: interactive analysis and visualization of alternative splicing in R
Alex C H Wong, Justin J-L Wong, John E J Rasko, Ulf Schmitz
Brief Bioinform. 2024 Jan; 25(1): bbad468. Published online 2023 Dec 27. doi: 10.1093/bib/bbad468
PMCID:
PMC10753292
ArticlePDF–3.6M
15.
Deep learning for genomics using Janggu
Wolfgang Kopp, Remo Monti, Annalaura Tamburrini, Uwe Ohler, Altuna Akalin
Nat Commun. 2020; 11: 3488. Published online 2020 Jul 13. doi: 10.1038/s41467-020-17155-y
PMCID:
PMC7359359
ArticlePDF–1.1M
16.
Discovering transcriptional regulatory elements from run-on and sequencing data using the web-based dREG gateway
Tinyi Chu, Zhong Wang, Shao-Pei Chou, Charles G. Danko
Curr Protoc Bioinformatics. Author manuscript; available in PMC 2020 Jun 1.
Published in final edited form as: Curr Protoc Bioinformatics. 2019 Jun; 66(1): e70. Published online 2018 Dec 27. doi: 10.1002/cpbi.70
PMCID:
PMC6584046
ArticlePDF–2.0M
17.
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
Brian J. Raney, Timothy R. Dreszer, Galt P. Barber, Hiram Clawson, Pauline A. Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S. Zweig, Donna Karolchik, W. James Kent
Bioinformatics. 2014 Apr 1; 30(7): 1003–1005. Published online 2013 Nov 13. doi: 10.1093/bioinformatics/btt637
PMCID:
PMC3967101
ArticlePDF–91K
18.
GeNemo: a search engine for web-based functional genomic data
Yongqing Zhang, Xiaoyi Cao, Sheng Zhong
Nucleic Acids Res. 2016 Jul 8; 44(Web Server issue): W122–W127. Published online 2016 Apr 20. doi: 10.1093/nar/gkw299
PMCID:
PMC4987887
ArticlePDF–2.0M
19.
scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data
Kai Hu, Haibo Liu, Nathan D. Lawson, Lihua Julie Zhu
Front Cell Dev Biol. 2022; 10: 981859. Published online 2022 Sep 27. doi: 10.3389/fcell.2022.981859
PMCID:
PMC9551270
ArticlePDF–6.1M
20.
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators
Marcin Piechota, Michal Korostynski, Joanna Ficek, Andrzej Tomski, Ryszard Przewlocki
BMC Bioinformatics. 2016; 17: 85. Published online 2016 Feb 12. doi: 10.1186/s12859-016-0938-4
PMCID:
PMC4751710
ArticlePDF–1.7M

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