Software Installed on Silo

Silo includes a variety of research software, including a variety of biomedical research software for researchers in the School of Medicine and Public Health. The following is a list of all of the software and packages that are currently installed.

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

 

 

If you are an SMPH researcher who anticipates using Silo, you can contact the SSCC Help Desk to request additional software.





Keywords:silo linsilo winsilo software stats   Doc ID:110541
Owner:Caitlin T.Group:Social Science Computing Cooperative
Created:2021-04-27 12:19 CDTUpdated:2021-04-27 12:24 CDT
Sites:Social Science Computing Cooperative
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