News: BioC2019 talks and workshops announced
gravatar for Levi Waldron
7 weeks ago by
Levi Waldron920
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron920 wrote:

BioC2019 (in New York City) talks and workshops have been announced, and will be greatly expanded compared to previous years. There are 21 user-oriented workshops in four tracks on June 25-26 (schedule):

  1. The Basics:
    • Bioconductor for Everyone
    • Fluent genomic workflows with plyranges and tximeta
    • Introduction to Bioconductor Annotation Resources
    • Public data resources and Bioconductor
  2. Single-cell analysis:
    • Effectively using the DelayedArray framework to support the analysis of large data sets
    • Orchestrating Single-Cell Analysis with Bioconductor: Overview and Workflows
    • Analysis of large single-cell RNA-seq datasets in R/Bioconductor
    • Analysis of multi-sample multi-group scRNA-seq data
    • iSEE: Interactive visualization of SummarizedExperiment objects
  3. RNAseq & Omics:
    • Workflow for Multi-omics Analysis with MultiAssayExperiment and curatedTCGAData
    • Bioinformatics tools to integrate and understand molecular changes associated with Immune Response, Stemness and Oncogenic processes: A PanCancer study
    • Working with open-source Human Microbiome Project Data: Efficient Data Access and Analysis Workflow
    • Using the recount2 resource and related tools
    • RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
    • Epidemiology for Bioinformaticians
  4. Genomics & Enrichment Analysis:
    • Tools for region-based genomic analysis
    • Copy number variation analysis with Bioconductor
    • ATAC-seq data quality control using the ATACseqQC package
    • Easy and efficient ensemble gene set testing with EGSEA
    • Functional enrichment analysis of high-throughput omics data
    • Integrative pathway analysis with pathwayPCA
    • Single sample gene set analysis

And 5 developer day workshops on June 24 (schedule):

  1. Bioconductor on Containers
  2. Common Workflow Language (a combined workshop of three developer groups spanning a wide range of tools and Cloud applications)
  3. Lazy representation of very large genomic data
  4. Cloud-scale genomic data science
  5. motifStack: plot multiple motifs in one figure

Finally, there will be a fourth day of more informal talks and discussion with founders of R and Bioconductor, in honor of Robert Gentleman's 60th birthday (June 27).

Early registration is available until May 24. Affordable hotels are still available, I recommend reserving those soon to avoid price increases. Many allow free cancellation in case you are not yet decided:

news bioc2019 • 398 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Levi Waldron920

Four sessions of contributed talks just posted: 1) single-cell, 2) statistical methods, 3) software infrastructure, 4) biological focus. In addition to the workshops. Early registration ends May 24! Draft schedule from :

Tuesday June 25:

: Single-cell theme -- room "A"

  • Robert A. Amezquita -- Orchestrating Single-Cell Analysis with Bioconductor
  • Helena L. Crowell -- Analysis of multi-sample multi-group scRNA-seq data
  • Shian Su -- CellBench: A Framework for Evaluating Single Cell Analysis Pipelines
  • Stephanie Hicks -- mbkmeans: fast clustering for single cell data using mini-batch k-means
  • Deepayan Sarkar -- Gene Set Enrichment Analysis with Multi-omics Data

: Statistical methods -- room "B"

  • Nima Hejazi -- Generalized Variance Moderation for Locally Efficient Estimation in High-Dimensional Biology
  • John Lawson -- Coordinate Covariation Analysis (COCOA): Understanding Interindividual Variation in Data with Genomic Coordinate s
  • Ingo Ruczinski -- Detection of rare disease variants in extended pedigrees using RVS
  • Svetlana Vinogradova -- ASER: eliminating transcriptome-wide batch effects results in higher precision in allele-specific expre ssion measurements
  • Katharina Imkeller -- Improving accuracy of phenotype detection in whole-genome CRISPR screens

Wednesday June 26:

: Software focus -- room "A"

  • Nitesh Turaga -- 3 reasons to "Bioconductor" on containers
  • Vincent Carey -- Bioconductor at "cloud scale"
  • Stuart Lee -- Tidy coverage analysis with superintronic and plyranges
  • Nathan Sheffield -- BiocProject, a new Bioconductor-oriented project management class
  • Karun Rajesh -- Storage and Analysis of Microbiome Quality Control Project Data through phyloseq Package
  • Ana Beatriz VillaseƱor-Altamirano -- PulmonDB with an accessible web interface of integrated and curated public transcriptomic data for the understanding of lung diseases
  • Christopher Wilks -- Snapcount: rapid and flexible querying of over 70,000 gene, exon, and splice junction expression summaries

: Biological focus -- room "B"

  • Benjamin Haibe-Kains -- mCI: Robust biomarker discovery from cancer pharmacogenomic data
  • Aedin Culhane -- Discovery of cancer immune molecular subtypes
  • Joselyn Cristina Chavez Fuentes -- A collaborative approach to improve access to bacterial regulatory networks using R/Bioconductor.
  • Robert Castelo -- RNA sequencing and mass spectometry proteomics of neonatal dried blood spots
  • Cesar Miguel Valdez Cordova -- histoneSig: working with continuous signal representations from the genome
  • Antonio Colaprico -- DeepBlueR and MoonlightR
  • Charlotte Soneson -- On the characterisation of complex transcriptomes with Nanopore native RNA sequencing
ADD REPLYlink written 5 weeks ago by Levi Waldron920
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