Epiviz: interactive visual analytics for functional genomics data

Chelaru, Florin; Smith, Llewellyn; Goldstein, Naomi; Bravo, Héctor Corrada

doi:10.1038/nmeth.3038

Cited by 60 publications

(48 citation statements)

References 19 publications

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“…Direct communication between R and genome browsers is implemented by the rtracklayer (for the UCSC Genome Browser) and SRAdb (for the Integrative Genomics Viewer) packages. The epivizr package implements interactive visualization of user data within a lightweight genome browser [8]. …”

Section: The User Perspectivementioning

confidence: 99%

Orchestrating high-throughput genomic analysis with Bioconductor

Huber

Carey

Gentleman³

et al. 2015

Nat Methods

3,237

2,492

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Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

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Section: The User Perspectivementioning

confidence: 99%

Orchestrating high-throughput genomic analysis with Bioconductor

Huber

Carey

Gentleman³

et al. 2015

Nat Methods

3,237

2,492

View full text Add to dashboard Cite

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“…The resulting bisulfite treated DNA was then subjected to the manufacture's protocol for the Illumina Infinium HumanMethylation450 BeadChip Kit. The data are publically available from GEO repository GSE53051, processed data can be browsed at [14].…”

Section: Microarray Processingmentioning

confidence: 99%

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

et al. 2014

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Background: One of the most provocative recent observations in cancer epigenetics is the discovery of large hypomethylated blocks, including single copy genes, in colorectal cancer, that correspond in location to heterochromatic LOCKs (large organized chromatin lysine-modifications) and LADs (lamin-associated domains). Methods: Here we performed a comprehensive genome-scale analysis of 10 breast, 28 colon, nine lung, 38 thyroid, 18 pancreas cancers, and five pancreas neuroendocrine tumors as well as matched normal tissue from most of these cases, as well as 51 premalignant lesions. We used a new statistical approach that allows the identification of large hypomethylated blocks on the Illumina HumanMethylation450 BeadChip platform.

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“…Genome browsers [13,21,29,52,55,12] visualize genome sequences. They compare genomes by visualizing the position of each nucleotide and consider a genome as a long and linear sequence of nucleotides.…”

Section: Event Sequence Comparisonmentioning

confidence: 99%

Cohort Comparison of Event Sequences with Balanced Integration of Visual Analytics and Statistics

Malik

Monroe

et al. 2015

Proceedings of the 20th International Conference on Intelligent User Interfaces

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Finding the differences and similarities between two datasets is a common analytics task. With temporal event sequence data, this task is complex because of the many ways single events and event sequences can differ between the two datasets (or cohorts) of records: the structure of the event sequences (e.g., event order, co-occurring events, or event frequencies), the attributes of events and records (e.g., patient gender), or metrics about the timestamps themselves (e.g., event duration). In exploratory analyses, running statistical tests to cover all cases is time-consuming and determining which results are significant becomes cumbersome. Current analytics tools for comparing groups of event sequences emphasize a purely statistical or purely visual approach for comparison. This paper presents a taxonomy of metrics for comparing cohorts of temporal event sequences, showing that the problem-space is bounded. We also present a visual analytics tool, CoCo (for "Cohort Comparison"), which implements balanced integration of automated statistics with an intelligent user interface to guide users to significant, distinguishing features between the cohorts. Lastly, we describe two early case studies: the first with a research team studying medical team performance in the emergency department and the second with pharmacy researchers.

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Epiviz: interactive visual analytics for functional genomics data

Cited by 60 publications

References 19 publications

Orchestrating high-throughput genomic analysis with Bioconductor

Orchestrating high-throughput genomic analysis with Bioconductor

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

Cohort Comparison of Event Sequences with Balanced Integration of Visual Analytics and Statistics

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