Biomedical Research Software on Silo

The following software has been installed on Silo to support biomedical research (see the SSCC Software Database for a complete list of software SSCC provides). If you are an SMPH researcher who anticipates using Silo, you can contact the SSCC Help Desk to request additional software.

R/RStudio with the following packages:

  • Bedr
  • Coloc
  • corrplot
  • dplyr
  • ggplot2
  • Gtools
  • MatrixEQTL
  • Mediation
  • PEER
  • Biobase
  • BiocManager
  • ChIPseeker
  • DESeq2
  • edgeR
  • GenomicRanges
  • GO.db
  • iBMQ
  • WGCNA
  • pROC
  • Robustbase
  • Tidyverse
  • UpSetR
  • impute
  • Limma
  • preprocessorcore
  • Qvalue
  • snpStats

Python 2.7 & 3.7, Anaconda Distribution, with the following packages:

  • Cutadapt
  • MACS2
  • Clipper
  • HTSeq

Other Software:

  • Matlab
  • Stata
  • SAS
  • Julia
  • Java
  • Netlogo
  • Git
  • Freesurfer
  • FSL
  • SPM
  • Samtools
  • bedtools
  • GATK
  • gingko (running locally)
  • Trim Galore!
  • TopHat
  • STAR
  • RSEM
  • Genome MuSiC
  • GATK
  • VarScan
  • PLINK
  • htslib
  • Eagle2
  • IMPUTE2
  • VCFtools
  • SNPEff
  • QTLtools
  • Qiime2
  • FastQC
  • Picard
  • Burrows-wheeler aligner (BWA)
  • Bowtie2





Keywords:Silo, SMPH, Research, Software, Medical   Doc ID:110462
Owner:Amanda T.Group:Social Science Computing Cooperative
Created:2021-04-22 15:52 CSTUpdated:2021-04-22 16:01 CST
Sites:Social Science Computing Cooperative
CleanURL:https://kb.wisc.edu/sscc/biomedical-research-software-on-silo
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