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Computational biology, software development, and R package development

Kevin Rue-Albrecht kevinrue

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Computational biology, software development, and R package development
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kevinrue / panel_RedDimHexbinPlot.R
Created December 9, 2019 15:51
Proof of concept for creating new panel types in iSEE 2.0
setClass("RedDimHexbinPlot", contains="RedDimPlot")
#' The reduced dimension hexbin plot panel
#'
#' Plots reduced dimensions summarizing points into hexagon bins.
#'
#' @section Constructor:
#' \code{RedDimHexbinPlot()} creates an instance of a RedDimHexbinPlot class.
#'
#' @author Kevin Rue
@kevinrue
kevinrue / iSEE_launcher.R
Created February 2, 2020 08:56 — forked from LTLA/iSEE_launcher.R
iSEE launching from link
############# The usual ################
library(scRNAseq)
# Example data ----
sce <- ReprocessedAllenData(assays="tophat_counts")
class(sce)
library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")
on:
push:
branches:
- master
pull_request:
branches:
- master
jobs:
build_check_deploy:
runs-on: ubuntu-latest
@kevinrue
kevinrue / snakemake_alevin_10x-renv-20200706.error
Created July 6, 2020 15:15
Error log for snakemake_alevin_10x using `renv`
* Restoring project ...
The following package(s) will be updated:
# Bioconductor =======================
- Biobase [* -> 2.48.0]
- BiocGenerics [* -> 0.34.0]
- BiocParallel [* -> 1.22.0]
- BiocVersion [* -> 3.11.1]
- Biostrings [* -> 2.56.0]
- DelayedArray [* -> 0.14.0]
@kevinrue
kevinrue / bioc-gitbook.css
Created July 8, 2020 08:26
CSS style sheet for Bioconductor GitBook
p.caption {
color: #777;
margin-top: 10px;
}
p code {
white-space: inherit;
}
pre {
word-break: normal;
word-wrap: normal;