Biomedical Research Software on Silo

The following software has been installed on Silo to support biomedical research. If you are an SMPH researcher who anticipates using Silo, you can contact the SSCC Help Desk to request additional software.

See the SSCC Software Database for a complete list of software the SSCC provides.

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
Owned by:
Russell D. in Social Science Computing Cooperative
Created:
2021-04-22
Updated:
2024-04-24
Sites:
Social Science Computing Cooperative
Clean URL:
https://kb.wisc.edu/sscc/biomedical-research-software-on-silo