Topics Map > Research Computing Support
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:
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Bedr Coloc corrplot dplyr ggplot2 Gtools MatrixEQTL Mediation PEER
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Biobase BiocManager ChIPseeker DESeq2 edgeR GenomicRanges GO.db iBMQ WGCNA |
pROC Robustbase Tidyverse UpSetR impute Limma preprocessorcore Qvalue snpStats |
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Python 2.7 & 3.7, Anaconda Distribution, with the following packages:
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Cutadapt MACS2 |
Clipper HTSeq |
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Other Software:
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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
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If you are an SMPH researcher who anticipates using Silo, you can contact the SSCC Help Desk to request additional software.