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Items: 1 to 20 of 143

1.

OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data.

Hu Y, Yan C, Hsu CH, Chen QR, Niu K, Komatsoulis GA, Meerzaman D.

Cancer Inform. 2014 Jan 16;13:13-20. doi: 10.4137/CIN.S13495. eCollection 2014.

2.

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.

Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M.

Bioinformatics. 2014 Jul 15;30(14):2076-8. doi: 10.1093/bioinformatics/btu168. Epub 2014 Mar 28.

3.

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.

Gu Z, Eils R, Schlesner M.

Bioinformatics. 2016 Sep 15;32(18):2847-9. doi: 10.1093/bioinformatics/btw313. Epub 2016 May 20.

PMID:
27207943
4.

HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data.

Gu Z, Eils R, Schlesner M.

Bioinformatics. 2016 Aug 1;32(15):2372-4. doi: 10.1093/bioinformatics/btw161. Epub 2016 Mar 24.

PMID:
27153599
5.

RCircos: an R package for Circos 2D track plots.

Zhang H, Meltzer P, Davis S.

BMC Bioinformatics. 2013 Aug 10;14:244. doi: 10.1186/1471-2105-14-244.

6.

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.

Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B.

Bioinformatics. 2013 Mar 1;29(5):666-8. doi: 10.1093/bioinformatics/bts708. Epub 2013 Jan 6.

7.

ggbio: an R package for extending the grammar of graphics for genomic data.

Yin T, Cook D, Lawrence M.

Genome Biol. 2012 Aug 31;13(8):R77. doi: 10.1186/gb-2012-13-8-r77.

8.

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Akman K, Haaf T, Gravina S, Vijg J, Tresch A.

Bioinformatics. 2014 Jul 1;30(13):1933-4. doi: 10.1093/bioinformatics/btu142. Epub 2014 Mar 10.

9.

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data.

Gel B, Serra E.

Bioinformatics. 2017 Oct 1;33(19):3088-3090. doi: 10.1093/bioinformatics/btx346.

PMID:
28575171
10.

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.

Chiu TP, Comoglio F, Zhou T, Yang L, Paro R, Rohs R.

Bioinformatics. 2016 Apr 15;32(8):1211-3. doi: 10.1093/bioinformatics/btv735. Epub 2015 Dec 14.

11.

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.

Bioinformatics. 2014 Nov 1;30(21):3136-8. doi: 10.1093/bioinformatics/btu397. Epub 2014 Jul 22.

12.

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 15;26(22):2902-3. doi: 10.1093/bioinformatics/btq531. Epub 2010 Sep 21.

13.

ADaCGH2: parallelized analysis of (big) CNA data.

Diaz-Uriarte R.

Bioinformatics. 2014 Jun 15;30(12):1759-61. doi: 10.1093/bioinformatics/btu099. Epub 2014 Feb 14.

14.

clusterProfiler: an R package for comparing biological themes among gene clusters.

Yu G, Wang LG, Han Y, He QY.

OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28.

15.

EBImage--an R package for image processing with applications to cellular phenotypes.

Pau G, Fuchs F, Sklyar O, Boutros M, Huber W.

Bioinformatics. 2010 Apr 1;26(7):979-81. doi: 10.1093/bioinformatics/btq046.

16.

flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies.

Rambaldi D, Pece S, Di Fiore PP.

Bioinformatics. 2014 Jul 15;30(14):2060-5. doi: 10.1093/bioinformatics/btu127. Epub 2014 Mar 27.

PMID:
24681909
17.

chimeraviz: a tool for visualizing chimeric RNA.

Lågstad S, Zhao S, Hoff AM, Johannessen B, Lingjærde OC, Skotheim RI.

Bioinformatics. 2017 Sep 15;33(18):2954-2956. doi: 10.1093/bioinformatics/btx329.

PMID:
28525538
18.

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.

Yu G, Wang LG, He QY.

Bioinformatics. 2015 Jul 15;31(14):2382-3. doi: 10.1093/bioinformatics/btv145. Epub 2015 Mar 11.

PMID:
25765347
19.

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.

Luo W, Brouwer C.

Bioinformatics. 2013 Jul 15;29(14):1830-1. doi: 10.1093/bioinformatics/btt285. Epub 2013 Jun 4.

20.

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.

Gel B, Díez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R.

Bioinformatics. 2016 Jan 15;32(2):289-91. doi: 10.1093/bioinformatics/btv562. Epub 2015 Sep 30.

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