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:
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
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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.