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NEWS
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CHANGES IN VERSION 1.22
-----------------------
OVERVIEW
The following enhancements have been added to systemPipeR.
- With the upgrades provided in this release, systemPipeR has become a much
more generic data analysis workflow environment that is no longer limited
to analyzing just NGS data. Now it can be efficiently used for data analysis
tasks in many omics areas, including genomics, proteomics, metabolomics and drug discovery.
- A workflow control class (SYSargsList) has been added allowing users to
manage multiple-step workflows from a single container. This way one can select
and execute multiple workflow steps with standard R subsetting syntax,
e.g. runWF[1:3].
- Various improvements have been added to systemPipeR’s new command-line
interface including the recently introduced SYSargs2 class that supports
the Common Workflow Language (CWL).
- Utilities have been added to visualize workflow designs and topologies with
different graphical layouts.
- Improvements have been added to monitor the run status of workflows as well
as better tracking of warning and error messages. This includes the generation
of both scientific and technical status reports.
CHANGES IN VERSION 1.3
----------------------
OVERVIEW
o systemPipeR is an R/Bioconductor package for building and running automated
analysis workflows for a wide range of next generation sequence (NGS)
applications. Important features include a uniform workflow interface
across different NGS 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. Efficient
handling of complex sample sets and experimental designs is facilitated by
a consistently implemented sample annotation infrastructure.
o The most important enhancements in the upcoming release of the package are
outlined below.
NGS WORKFLOWS
o Added new end-to-end workflows for 3 additional NGS application areas:
- Ribo-Seq and polyRibo-Seq
- ChIP-Seq
- VAR-Seq
The previous version of systemPipeR included only a complete workflow for
RNA-Seq.
o Added the data package 'systemPipeRdata' to generate systemPipeR workflow
environments with a single command (genWorkenvir) containing all parameter
files and sample data required to quickly test and run workflows. This
change will also allow evaluation of much more code examples in the
vignettes during the package build/test process than this was possible in
the past.
o About 20 new functions have been added to the package. Some examples are:
- Read pre-processor function with support for SE and PE reads
- Parallelization option of detailed FASTQ quality reports
- Read distribution plots across all features available in a
genome annotation (see ?featuretypeCounts)
- Visualization of coverage trends along transcripts summarized
for any number of transcripts (see ?featureCoverage)
- Functionalities to predict uORFs/sORFs and to use them for expression profiling
- Differential expression/binding analysis includes now DESeq2 as
well as edgeR
o Added param templates for additional command-line software including, but
not limited to: BWA-MEM, GATK, BCFtools, MACS2
o Adoption of R Markdown for main vignette. Future plans are to provide for
all workflows the report templates in both formats: Latex/PDF and
R_Markdown/HTML.
WORFLOW FRAMEWORK
o Simplified design of complex analysis workflows. Workflows can now include
any number or combination of R and/or command-line steps
o Improvements to workflow automation and parallelization on single
machines and computer clusters. This also includes now many additional
parallelization examples in the workflow vignettes.