R-universe search: systempiper

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bioc

systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.

Maintained by Thomas Girke. Last updated 5 months ago.

genetics infrastructure dataimport sequencing rnaseq riboseq chipseq methylseq snp geneexpression coverage genesetenrichment alignment qualitycontrol immunooncology reportwriting workflowstep workflowmanagement

61.8 match 53 stars 11.56 score 344 scripts 3 dependents

bioc

systemPipeShiny:systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS’ current functionalities include: (a) interactive creation of experimental designs and metadata using an easy to use tabular editor or file uploader; (b) visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows; (d) access to a wide range of data processing routines; (e) and an extendable set of visualization functionalities. Complex visual results can be managed on a 'Canvas Workbench’ allowing users to organize and to compare plots in an efficient manner combined with a session snapshot feature to continue work at a later time. The present suite of pre-configured visualization examples. The modular design of SPR makes it easy to design custom functions without any knowledge of Shiny, as well as extending the environment in the future with contributions from the community.

Maintained by Le Zhang. Last updated 5 months ago.

shinyapps infrastructure dataimport sequencing qualitycontrol reportwriting experimentaldesign clustering bioconductor bioconductor-package data-visualization shiny systempiper

10.8 match 33 stars 7.03 score 36 scripts

bioc

systemPipeTools:Tools for data visualization

systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives.

Maintained by Daniela Cassol. Last updated 5 months ago.

infrastructure dataimport sequencing qualitycontrol reportwriting experimentaldesign clustering differentialexpression multidimensionalscaling principalcomponent

2.1 match 4.00 score 4 scripts