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https://github.com/bihealth/rseasnap

Uncomplicated access to sea-snap objects from R

https://github.com/bihealth/rseasnap

Science Score: 13.0%

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Repository

Uncomplicated access to sea-snap objects from R

Basic Info
  • Host: GitHub
  • Owner: bihealth
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 1.03 MB
Statistics
  • Stars: 0
  • Watchers: 8
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

Rseasnap

A collection of functions which make it easy to access the files and objects created by the sea-snap DE pipeline.

Why Rseasnap:

  • shortcuts for accessing pipeline objects
  • produce plots on the fly
  • easier to work with multiple pipelines

Why not part of sea-snap distribution (e.g. as R scripts):

  • better documentation
  • can be used for other tasks as well
  • easier to maintain

Installation

You can install the current version of Rseasnap as follows:

r library(devtools) install_github("bihealth/Rseasnap")

Alternatively, clone the git repo and install from the clone directory, e.g.

r system("git clone git@github.com:bihealth/Rseasnap.git") devtools::install_git("Rseasnap")

Quickstart

Load the DE pipeline object:

r library(Rseasnap) pip <- load_de_pipeline("DE_config.yaml")

Once the YAML file is loaded into the object, you can use it to access various objects and files:

``` r

get the counts

counts <- get_counts(pip)

get the expression data

expr <- get_exprs(pip)

show contrast names

getcontrastnames(pip)

get the DE results

res <- get_contrasts(pip)

get the gene annotation file

annot <- get_annot(pip)

get the covariate file

covar <- get_covariates(pip) ```

Owner

  • Name: Berlin Institute of Health
  • Login: bihealth
  • Kind: organization

BIH Core Unit Bioinformatics & BIH HPC IT

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