News! eyeIntegration version 1.0 went live early this year (2019-01-16) and recently was accepted for publication in IOVS. In celebration of the news, I’m posting a small series of posts about the genesis, development, upgrades, and future of eyeIntegration.
You can find our latest manuscript on bioRxiv. The latest update should go live soon.
Background eyeIntegration was developed to serve as a quick and easy to use normal gene expression portal in eye tissues.
This post is a continuation from here.
Really important stuff I learned to make a performant web site in Shiny After a few months of tinkering I had a working web app on my local computer, which is a 32GB of RAM, 1TB SSD Mac Pro trashcan. All of the data objects were .Rdata, which were load() when the site was initialized. This was fine in the beginning and in fact the shiny site was deployed with this structure in May of 2017.
Variant Discovery and Genome Assembly Melissa Wilson Sayres Prithika Sritharan (Dicks) Zemin Ning (Durbin) Variant Discovery and Genome Assembly Melissa Wilson Sayres Sex Differences in Reference Genome Affect Variant Calling and Differential Expression
X and Y homology dotplot
a few regions of alignment (PAR) @sexchrlab
doi.org/10.1101/346940
https://www.biorxiv.org/content/early/2018/07/18/346940 preprint on correct tech biases on sex chr in NGS data infer sex chromosome complement pointing out regions on autosomes with sex chr - like alignment which is screwing up read balance which presumably could influence variant calling chrY var calls will have many errors
Day 3 Rafael Irizarry Keynote Session 4: Transcriptomics, Alternative Splicing and Gene Predictions Mark Robinson (Robinson) Hagen Tilgner (Tilgner) Nikka Keivanfar (Church, 10X) Koen Van den Berge (Clement) Barbara Englehardt (Englehardt) Jeff Gaither (White) Fiona Dick (Tzoulis) Epigenetics and non-coding genome Jordana Bell (Bell) Wouter Meuleman (Stamatoyannopoulos) Maša Roller (Flicek) Alexander Suh (Suh) Raquel Garcia-Perez (Juan) Day 3 Very sparse and poorly written notes covering #GI2018.
Day Two Personal and Medical Genomics Katie Pollard Keynote Sri Kosuri (Kosuri) Patrick Brennan (Nationwide Children’s) Kaitlin Samocha (Hurles) Tracy Ballinger (Semple) Lucia Spangenberg (Naya) Comparative, Evolutionary, Metagenomics Ellen Leffler (Kwiatkowski) Luca Penso-Dolfin (Di Palma) Mario Caccamo (NIAB) Carla Cummins (Flicek) Day Two Personal and Medical Genomics Very sparse and poorly written notes covering #GI2018.
Typos everywhere. Things may change dramatically over time as I scan back through notes.
Intro 2018-09-17 Sarah Teichmann (Teichmann Lab) Girgio Gonnella (Stefan Kurtz) Luke Zappia (Oshlack?) Laura Huerta (Papatheodorou) Casey Greene (Greene) Sergei Yakneen Intro Very sparse and poorly written notes covering #GI2018.
Typos everywhere. Things may change dramatically over time as I scan back through notes.
I’ve tried to respect #notwitter. Will be updated periodically.
Speaker (Lab | Group)
BOLDED is voice
2018-09-17 Sarah Teichmann (Teichmann Lab) Cell Atlas Technologies and the Maternal-Fetal Interface
Background There are several popular naming systems for (human) genes:
RefSeq (NM_000350) Ensembl (ENSG00000198691) HGNC Symbol (ABCA4) Entrez (24) Given enough time in #bioinformatics, you will have to do every possible combination of conversions.
This post will very briefly explain the most expedient way to automatically convert between these formats with R.
More exhaustive resources http://crazyhottommy.blogspot.com/2014/09/converting-gene-ids-using-bioconductor.html
https://davetang.org/muse/2013/11/25/thoughts-converting-gene-identifiers/
Ensembl <-> HGNC <-> Entrez Stephen Turner has built a small set of data frames (well, tibbles) with core information, including transcript <-> gene info.
Introduction Data processing Load data Peek at expression Peek at metadata Brief outline on how the RNA-seq data was processed before we see it Load libraries Create a Sample - Sample distance heatmap Easy heatmap with ComplexHeatmap Complex heatmap Finished heatmap Gene Heatmaps A bit simpler Session Info Introduction Heatmaps are a core competency for a bioinformatician. They are a compact way to visually demonstrate relationships and changes in values across conditions.
What is this? Since I keep opening up random recent Rmarkdown documents to copy the header to paste into my next document, I figure it would be more efficient to just make a post I could reach from anywhere (with an internet connection).
Copy / paste: --- title: THE TITLE author: David McGaughey date: '`r format(Sys.Date(), "%Y-%m-%d")`' output: html_notebook: theme: flatly toc: true code_folding: hide --- ```{r, message=F, warning=F, include=F} # Load Libraries without printing any warnings or messages library(tidyverse) ``` # Session Info