/bio-class-age

Repository for building virtual classroom for biology students - Analysis of gene expression class

Primary LanguageShellOtherNOASSERTION

bio-class-age

Dockerfile for building virtual classroom for biology students - Analysis of gene expression class

Usage

This image is intended for Analysis of gene expression class tought at Institute of Molecular Genetics of the ASCR, v. v. i.

Software

  • BCFtools
  • Bioconductor
  • BSMAP
  • BWA
  • cutadapt
  • FastQC
  • gmap
  • HTSlib
  • MultiQC
  • Picard-tools
  • RStudio Desktop + Server
  • salmon
  • samtools
  • SRA Toolkit
  • Trimmomatic

Bioconductor modules

  • Biobase
  • BiocParallel
  • DESeq2
  • DT
  • GOstats
  • GOsummaries
  • GenomicAlignments
  • GenomicFeatures
  • Heatplus
  • KEGG.db
  • PoiClaClu
  • RColorBrewer
  • ReportingTools
  • Rsamtools
  • Seurat
  • affy
  • airway
  • annotate
  • arrayQualityMetrics
  • beadarray
  • biomaRt
  • dendextend
  • gdata
  • genefilter
  • goseq
  • gplots
  • gtools
  • hgu133plus2.db
  • hgu133plus2cdf
  • hgu133plus2probe
  • hwriter
  • illuminaHumanv3.db
  • lattice
  • limma
  • lumi
  • made4
  • oligo
  • org.Hs.eg.db
  • org.Mm.eg.db
  • org.Rn.eg.db
  • pander
  • pd.rat230.2
  • pheatmap
  • preprocessCore
  • qvalue
  • rat2302.db
  • rmarkdown
  • sva
  • tidyverse
  • vsn
  • xtable

Image

RStudio server is started on container start. User can log-in via username: student and password set via PASSWORD container environment variable. To access RStudio server container must be bind on port 8787.