Requests for default Python/R packages and libraries Pinned

Post author
Jason Cerrato

If there is a package or library you would like to see made part of the default Terra runtime configurations, please make a comment below with the name of the software (Python or R), the package or library name, and the function of the package or library (what kind of analysis would this be necessary for?).

If the package or library has already been requested, please upvote that comment so the Terra team can effectively prioritize these requests based on popularity/need.

Example:

Software: R

Package: Seurat

Function: Single-cell analysis

Comments

6 comments

  • Comment author
    lck
    • Edited

    Software: R

    Package: tableone

    Function: Easy creation of "table one"-type tables for analyses

    (Alternatively, I'd love a way to install this myself in a notebook. It fails, I think because I can't install RcppEigen for some reason. Thanks!)

    1
  • Comment author
    Rachelly Normand

    Software: Python

    Package: Scanpy

    Function: Single-cell analysis

     
    1
  • Comment author
    Yury O. Nunez Lopez

    Software: R

    Package: systemPipeR

    Function: Provides flexible utilities for designing, building and running automated end-to-end analysis workflows for a wide range of research applications, including next-generation sequencing (NGS) experiments, such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq (H Backman and Girke 2016). Important features include a uniform workflow interface across different data analysis applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. The latter supports interactive job submissions and batch submissions to queuing systems of clusters. (Extracted from systemPipeR: Workflow and Visualization Toolkit (bioconductor.org)) 

    1
  • Comment author
    Stephen Fleming

    Software: R

    Package: `sudo apt-get install libopenblas-base`

    (Not really an R package, but this would be software installed in the R base image for Terra.)

    Function: automatic multi-core operations when possible.  With tools like `limma` and `voom` I see a 16x speedup on a 16 CPU machine, which is awesome.

    More information here:

    https://github.com/DataBiosphere/terra-docker/issues/210#issuecomment-832231997

    1
  • Comment author
    Josh Evans

    Hi Yury and Stephen,

    Thank you both for writing in! I've sent these request to our development team for consideration, and I'll be happy to follow up with you if these features gets built.

    Kind regards,

    Josh​ 

    1
  • Comment author
    Ally Eran

    Hi Josh Evans,

    I can't install RcppEigen, as lck mentioned. That's needed to install scSHC (Significance Analysis for Clustering Single-Cell RNA-Sequencing Data). Could you please enable RcppEigen installation or otherwise install scSHC? (https://github.com/igrabski/sc-SHC)

    Thanks!

    Ally

    0

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