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