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Updates related to Bioconductor 3.12 for other LIBD members


Leonardo Collado-Torres

November 20, 2020

More Decks by Leonardo Collado-Torres

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  1. Bioconductor 3.12 Leonardo Collado Torres lcolladotor.github.io 2020-11-20

  2. LIEBER INSTITUTE for BRAIN DEVELOPMENT http://bioconductor.org/about/

  3. LIEBER INSTITUTE for BRAIN DEVELOPMENT http://bioconductor.org/news/bioc_3_12_release/

  4. LIEBER INSTITUTE for BRAIN DEVELOPMENT https://twitter.com/mikelove/status/1324348808327794689?s=20

  5. LIEBER INSTITUTE for BRAIN DEVELOPMENT https://twitter.com/LIBDrstats/status/1324861604488503300?s=20

  6. LIEBER INSTITUTE for BRAIN DEVELOPMENT New packages I was involved

    in biocthis: R package development megadepth: faster coverage summaries over genomic regions for BigWig / BAM files; with David Zhang (UCL) & Christopher Wilks + Ben Langmead (JHU CS) recount3: 750,000+ public human/mouse RNA-seq dasper: interpreting exon-exon junctions in the clinic; David Zhang & Mina Ryten (UCL)
  7. LIEBER INSTITUTE for BRAIN DEVELOPMENT Highlighted by Mike Love (subset)

    bambu: multi-sample transcript discovery and quantification using long read RNA-Seq data pipeComp: facilitate the comparison of pipelines involving various steps and parameters recountmethylation: similar to recount2 but for methylation data; Sean Maden & Abhinav Nellore velociraptor: Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data
  8. LIEBER INSTITUTE for BRAIN DEVELOPMENT Highlighted in the LIBD rstats

    club (subset) BayesSpace: clustering method for Visium data (discussed in our spatial journal club) DegNorm: base-pair coverage normalization of RNA-seq data (presentation by Josh Stolz https://www.youtube.com/watch?v=YF5jw--Ky-g ) Nebulosa: visualization method for dense clustered data (tSNE/UMAP; LIBD rstats club today) famat: create shiny (interactive) visualizations for gene pathways, GO terms and more SpatialExperiment: for storing Visium data (we are involved in planning updates for it)
  9. LIEBER INSTITUTE for BRAIN DEVELOPMENT https://www.youtube.com/c/LeonardoColladoTorres/playlists

  10. LIEBER INSTITUTE for BRAIN DEVELOPMENT How I’m trying to keep

    myself updated • LIBD rstats club: Fridays 1pm, open to LIBD & collaborators https://groups.google.com/g/libd-rstats-club + upload to YouTube https://www.youtube.com/c/LeonardoColladoTorres/playlists • Leo’s team meeting (closed; Wednesdays 3pm): we record our journal/software club portion and upload to YouTube • Spatial journal club (closed; bi-weekly on Thursdays 11 am): no recordings