199 related articles for article (PubMed ID: 34695109)
1. NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.
Su S; Gouil Q; Blewitt ME; Cook D; Hickey PF; Ritchie ME
PLoS Comput Biol; 2021 Oct; 17(10):e1009524. PubMed ID: 34695109
[TBL] [Abstract][Full Text] [Related]
2. DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation.
Liu Y; Rosikiewicz W; Pan Z; Jillette N; Wang P; Taghbalout A; Foox J; Mason C; Carroll M; Cheng A; Li S
Genome Biol; 2021 Oct; 22(1):295. PubMed ID: 34663425
[TBL] [Abstract][Full Text] [Related]
3. BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data.
Hu K; Ting AH; Li J
BMC Bioinformatics; 2015 Jul; 16():220. PubMed ID: 26163275
[TBL] [Abstract][Full Text] [Related]
4. Whole human genome 5'-mC methylation analysis using long read nanopore sequencing.
Silva C; Machado M; Ferrão J; Sebastião Rodrigues A; Vieira L
Epigenetics; 2022 Dec; 17(13):1961-1975. PubMed ID: 35856633
[TBL] [Abstract][Full Text] [Related]
5. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Lee I; Razaghi R; Gilpatrick T; Molnar M; Gershman A; Sadowski N; Sedlazeck FJ; Hansen KD; Simpson JT; Timp W
Nat Methods; 2020 Dec; 17(12):1191-1199. PubMed ID: 33230324
[TBL] [Abstract][Full Text] [Related]
6. RepViz: a replicate-driven R tool for visualizing genomic regions.
Faux T; Rytkönen KT; Laiho A; Elo LL
BMC Res Notes; 2019 Jul; 12(1):441. PubMed ID: 31324268
[TBL] [Abstract][Full Text] [Related]
7. Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase.
Akbari V; Garant JM; O'Neill K; Pandoh P; Moore R; Marra MA; Hirst M; Jones SJM
Genome Biol; 2021 Feb; 22(1):68. PubMed ID: 33618748
[TBL] [Abstract][Full Text] [Related]
8. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.
Catoni M; Tsang JM; Greco AP; Zabet NR
Nucleic Acids Res; 2018 Nov; 46(19):e114. PubMed ID: 29986099
[TBL] [Abstract][Full Text] [Related]
9. Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing.
Yue X; Xie Z; Li M; Wang K; Li X; Zhang X; Yan J; Yin Y
Nat Commun; 2022 Dec; 13(1):7939. PubMed ID: 36566265
[TBL] [Abstract][Full Text] [Related]
10. MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.
Lienhard M; Grimm C; Morkel M; Herwig R; Chavez L
Bioinformatics; 2014 Jan; 30(2):284-6. PubMed ID: 24227674
[TBL] [Abstract][Full Text] [Related]
11. Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.
Akman K; Haaf T; Gravina S; Vijg J; Tresch A
Bioinformatics; 2014 Jul; 30(13):1933-4. PubMed ID: 24618468
[TBL] [Abstract][Full Text] [Related]
12. Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS.
Liu Y; Cheng J; Siejka-Zielińska P; Weldon C; Roberts H; Lopopolo M; Magri A; D'Arienzo V; Harris JM; McKeating JA; Song CX
Genome Biol; 2020 Mar; 21(1):54. PubMed ID: 32127008
[TBL] [Abstract][Full Text] [Related]
13. BRGenomics for analyzing high-resolution genomics data in R.
DeBerardine M
Bioinformatics; 2023 Jun; 39(6):. PubMed ID: 37208173
[TBL] [Abstract][Full Text] [Related]
14. Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing.
Sakamoto Y; Zaha S; Nagasawa S; Miyake S; Kojima Y; Suzuki A; Suzuki Y; Seki M
Nucleic Acids Res; 2021 Aug; 49(14):e81. PubMed ID: 34019650
[TBL] [Abstract][Full Text] [Related]
15. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences.
Hon J; Martínek T; Rajdl K; Lexa M
Bioinformatics; 2013 Aug; 29(15):1900-1. PubMed ID: 23709494
[TBL] [Abstract][Full Text] [Related]
16. Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.
Toedling J; Ciaudo C; Voinnet O; Heard E; Barillot E
Bioinformatics; 2010 Nov; 26(22):2902-3. PubMed ID: 20861030
[TBL] [Abstract][Full Text] [Related]
17. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
Meng J; Lu Z; Liu H; Zhang L; Zhang S; Chen Y; Rao MK; Huang Y
Methods; 2014 Oct; 69(3):274-81. PubMed ID: 24979058
[TBL] [Abstract][Full Text] [Related]
18. Bigmelon: tools for analysing large DNA methylation datasets.
Gorrie-Stone TJ; Smart MC; Saffari A; Malki K; Hannon E; Burrage J; Mill J; Kumari M; Schalkwyk LC
Bioinformatics; 2019 Mar; 35(6):981-986. PubMed ID: 30875430
[TBL] [Abstract][Full Text] [Related]
19. Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing.
Giesselmann P; Brändl B; Raimondeau E; Bowen R; Rohrandt C; Tandon R; Kretzmer H; Assum G; Galonska C; Siebert R; Ammerpohl O; Heron A; Schneider SA; Ladewig J; Koch P; Schuldt BM; Graham JE; Meissner A; Müller FJ
Nat Biotechnol; 2019 Dec; 37(12):1478-1481. PubMed ID: 31740840
[TBL] [Abstract][Full Text] [Related]
20. GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data.
Marini F; Ludt A; Linke J; Strauch K
BMC Bioinformatics; 2021 Dec; 22(1):610. PubMed ID: 34949163
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
