ezRun

An R meta-package for the analysis of Next Generation Sequencing data.

The version of ezRun package is bound to the release of Bioconductor development branch.

Dependencies of Python packages

pip3 install velocyto magic-impute
pip3 install multiqc

Dependencies of R/Bioconductor packages

packages <- c("testthat", "knitr", "goseq", "ChIPpeakAnno", 
              "DESeq2", "TEQC", "pathview", "reshape2", 
              "vsn", "Rsubread", "preprocessCore", "wesanderson",
              "RCurl", "caTools", "matrixStats", "Repitools", "DT", 
              "htmltools", "biomaRt", "grid", "gridExtra",
              "RColorBrewer", "WGCNA", "plyr", "pvclust", "parallel", 
              "Biostrings", "Rsamtools", "Hmisc", "XML", 
              "stringr", "GenomicAlignments", "GenomicFeatures",
              "GenomicRanges", "ShortRead", "Gviz", "gplots", "GO.db", 
              "GOstats", "annotate", "bitops", "edgeR", "limma", "S4Vectors",
              "VariantAnnotation", "rmarkdown", "plotly", "scran",
              "data.table", "kableExtra", "htmlwidgets",
              "webshot", "clusterProfiler", "dupRadar", "pheatmap",
              "taxize", "SingleCellExperiment", "SummarizedExperiment",
              "scater", "DropletUtils", "shiny", "heatmaply", "readxl",
              "readr", "dplyr", "shinycssloaders", "shinyjs", "slingshot",
              "Rmagic", "reticulate", "viridis", "Seurat", "tidyverse",
              "httr", "jsonlite", "xml2", "writexl", "zip")
packages <- setdiff(packages, rownames(installed.packages()))
BiocManager::install(packages)

remotes::install_github("velocyto-team/velocyto.R")

Dependencies of external software

• bwa, bowtie, bowtie2, STAR, picard, sambamba, samtools, igvtools
• lsof

Installation of the development version of ezRun from github

remotes::install_github("uzh/ezRun")

Development of ezRun package at FGCZ environment

During development at FGCZ, load the external tools from the module system (module avail / module load Aligner/... Tools/...) before starting R. There is no ezRun conda environment.

Coding style

Do follow the guidelines in CodingStyle.md