Title: RIS-Vetted Application Containers  
Owner: RIS-SVC-conf-publish
Creator: RIS-SVC-conf-publish Aug 19, 2021
Last Changed by: RIS-SVC-conf-publish Jun 06, 2023
Tiny Link: (useful for email) https://washu.atlassian.net/wiki/x/wIb7Cg
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RIS Knowledge Base (15)
    Page: cisTEM Dockerimage
    Page: Compute FAQ
    Page: Compute Topics
    Page: Create Custom conda Environment
    Page: Integrative Genomics Viewer (IGV)
    Page: MATLAB Quick Start
    Page: noVNC Docker Image
    Page: NVIDIA Workshop - September 2020
    Page: RIS Compute 104
    Page: RIS R Workshop
    Page: RIS Services User Manual
    Page: RStudio
    Page: Stata Quick Start
    Page: TensorFlow Quick Start
    Page: Web Development Container
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Jun 06, 2023 08:13 RIS-SVC-conf-publish View Changes
Jun 05, 2023 15:33 RIS-SVC-conf-publish View Changes
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May 25, 2023 09:31 RIS-SVC-conf-publish View Changes
May 25, 2023 08:45 RIS-SVC-conf-publish  
Outgoing Links
External Links (123)
    https://bioconda.github.io/recipes/picard/README.html
    circos.ca/
    https://en.wikipedia.org/wiki/Go_%28programming_language%29
    https://docs.microsoft.com/en-us/dotnet/core/
    https://satijalab.org/seurat/
    https://julialang.org/
    compute1-exec-nn.ris.wustl.edu:8888/
    https://bioconda.github.io/recipes/tophat/README.html
    https://hub.docker.com/r/rocker/verse
    https://bioconductor.org/packages/3.10/bioc/html/SingleR.ht…
    https://www.ncbi.nlm.nih.gov/pubmed/23104886
    https://bioconda.github.io/recipes/bedtools/README.html
    https://bioconda.github.io/recipes/oncotator/README.html
    https://valgrind.org/
    https://cran.r-project.org/doc/FAQ/R-FAQ.html#What-is-R_003…
    https://bioconductor.org/packages/3.10/bioc/html/IRanges.ht…
    https://rstudio.com/
    https://bioconda.github.io/recipes/bcftools/README.html
    www.novocraft.com/products/novoalign/
    https://bioconductor.org/packages/release/bioc/html/monocle…
    https://bioconda.github.io/recipes/bwa/README.html
    https://hub.docker.com/_/perl
    https://hub.docker.com/r/continuumio/anaconda
    compute1-exec-nn.ris.wustl.edu:8001/
    https://hub.docker.com/r/lifebitai/prsice2
    https://bioconductor.org/packages/3.10/bioc/html/GenVisR.ht…
    https://docs.ris.wustl.edu/doc/compute/recipes/port-forward…
    https://hub.docker.com/_/r-base
    https://bioconda.github.io/recipes/bioconductor-edger/READM…
    https://qiime2.org/
    https://jupyter-docker-stacks.readthedocs.io/en/latest/usin…
    https://hub.docker.com/r/cumulusprod/cellranger
    https://github.com/etal/cnvkit
    https://shiny.rstudio.com/
    https://bioconductor.org/packages/3.10/bioc/html/Organism.d…
    https://github.com/genome/breakdancer
    https://hub.docker.com/r/skwalker/plink2
    https://bioconda.github.io/recipes/bioconductor-organism.dp…
    https://hub.docker.com/r/gromacs/gromacs
    https://rapids.ai/about.html
    https://bioconductor.org/packages/3.10/bioc/html/edgeR.html
    https://hub.docker.com/_/python
    https://bioconda.github.io/recipes/strelka/README.html
    https://jupyter.org
    https://hub.docker.com/r/continuumio/anaconda3
    https://bioconda.github.io/recipes/cufflinks/README.html
    compute1-exec-nn.ris.wustl.edu
    https://github.com/lh3/bwa
    https://www.htslib.org/
    broadinstitute.github.io/picard/
    https://iterm2.com/documentation.html
    https://hub.docker.com/_/julia
    https://bioconda.github.io/recipes/blast/README.html
    https://bioconda.github.io/recipes/manta/README.html
    bowtie-bio.sourceforge.net/bowtie2/index.shtml
    https://hub.docker.com/r/glotzerlab/software/
    https://quay.io/repository/biocontainers/bowtie2?tab=info
    https://www.ncbi.nlm.nih.gov/books/NBK158900/
    https://hub.docker.com/r/rocker/shiny
    https://zzz.bwh.harvard.edu/plink/plink2.shtml
    https://learn.microsoft.com/en-us/windows-server/administra…
    cole-trapnell-lab.github.io/cufflinks/
    https://www.prsice.info/
    https://iterm2.com/downloads.html
    zzz.bwh.harvard.edu/plink/
    https://hub.docker.com/_/microsoft-dotnet-core-sdk/
    https://registry.hub.docker.com/r/bioinstaller/annovarr
    https://bioconda.github.io/recipes/bioconductor-maftools/RE…
    https://hub.docker.com/_/golang
    https://vimhelp.org/
    https://docs.ris.wustl.edu/doc/compute/recipes/tools/ris-rs…
    https://en.wikipedia.org/wiki/OpenJDK
    gmt.genome.wustl.edu/packages/pindel/index.html
    https://bioconda.github.io/recipes/ensembl-vep/README.html
    https://bioconda.github.io/recipes/bioconductor-genvisr/REA…
    dkoboldt.github.io/varscan/
    https://bioconda.github.io/recipes/bioconductor-cn.mops/REA…
    https://bioconda.github.io/recipes/pindel/README.html
    https://support.10xgenomics.com/single-cell-gene-expression…
    https://bioconductor.org/packages/3.10/bioc/html/maftools.h…
    https://www.ncbi.nlm.nih.gov/pubmed/18440982
    snpeff.sourceforge.net/SnpSift.html
    https://software.broadinstitute.org/cancer/cga/oncotator
    https://hub.docker.com/r/koetjen/rstudio
    https://bioconda.github.io/recipes/bioconductor-iranges/REA…
    https://bioconda.github.io/recipes/varscan/README.html
    compute1-exec-nn.ris.wustl.edu:8888
    https://bioconda.github.io/recipes/star/README.html
    https://bioconda.github.io/recipes/circos/README.html
    ccb.jhu.edu/software/tophat/index.shtml
    https://github.com/Illumina/strelka
    https://hub.docker.com/r/greymail/gcc-cmake-valgrind
    https://bioconda.github.io/recipes/bioconductor-monocle/REA…
    https://bioconda.github.io/recipes/bioconductor-singler/REA…
    https://bioconda.github.io/recipes/snpsift/README.html
    https://bioconda.github.io/recipes/vcftools/README.html
    https://hub.docker.com/r/jupyter/datascience-notebook
    https://hub.docker.com/_/openjdk
    https://github.com/ekg/freebayes
    https://bioconda.github.io/recipes/hisat2/README.html
    https://docs.ris.wustl.edu/doc/compute/recipes/tools/novnc-…
    https://bioconda.github.io/recipes/bioconductor-genomicrang…
    https://ccb.jhu.edu/software/hisat2/index.shtml
    https://bioconda.github.io/recipes/freebayes/README.html
    https://bioconda.github.io/recipes/samtools/README.html
    https://bioconda.github.io/recipes/cnvkit/README.html
    https://bedtools.readthedocs.io/en/latest/
    glotzerlab.engin.umich.edu/home/resources/
    https://ipython.readthedocs.io/en/stable/install/index.html…
    velocyto.org/
    https://bioconda.github.io/recipes/bamtools/README.html
    bowtie-bio.sourceforge.net/index.shtml
    https://bioconda.github.io/recipes/plink/README.html
    https://bioconda.github.io/recipes/bowtie/README.html
    https://hub.docker.com/r/genomicpariscentre/velocyto
    https://hub.docker.com/r/rapidsai/rapidsai
    https://bioconda.github.io/recipes/seurat-scripts/README.ht…
    www.gromacs.org/About_Gromacs
    https://bioconda.github.io/recipes/novoalign/README.html
    https://bioconda.github.io/recipes/breakdancer/README.html
    https://bioconductor.org/packages/3.10/bioc/html/GenomicRan…
    https://hub.docker.com/r/qiime2/core
    https://learn.microsoft.com/en-us/windows/terminal/install
RIS Knowledge Base (3)     Page: RIS-Supported Application Containers
    Page: RStudio
    Page: Docker Wrapper Environment Variables