Biomedical Research Software on Silo
The following software has been installed on Silo to support biomedical research (see the SSCC Software Database for a complete list of software SSCC provides). If you are an SMPH researcher who anticipates using Silo, you can contact the SSCC Help Desk to request additional software.
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