README.md
In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data
RNASeqPipelineR
Streamline the processing of RNASeq data
System requirements
You need the following R packages:
data.table
GEOquery
RSQLite
SRAdb
The following command line utilities:
SRA Toolkit (from NCBI http://www.ncbi.nlm.nih.gov/books/NBK158900/)
ascp (Aspera scp client, distributed with Aspera Connect)
RSEM (http://deweylab.biostat.wisc.edu/rsem/)
bowtie2 (http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html)
BioConductor (http://www.bioconductor.org/)
MiTCR (http://mitcr.milaboratory.com/)
fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
PEAR (http://sco.h-its.org/exelixis/web/software/pear/) for paired end assembly
GEOQuery from BioConductor
Development Notes
Still under development.
Why?
The basic idea behind the package is to held organize and manage the pipeline of processing fastq files, whether they come from data on GEO, or whether they are provided by collaborators.
The package creates a standard directory structure for each project and tracks where files are stored, how they are processed,and generates a report describing what tools are used in the processing.
Output files are annotated and stored in standard locations and convenience functions are provided to construct ExpressionSet or SingleCellAssay objects with full feature and phenotypic (pData) annotations.
When working collaboratively it's important not to duplicate effort. Different people working on the same data set need to ensure that they are working with data that has been processed the same way, and if there are multiple analyses, having that data located and processed in a predictable way and stored in a standard locations becomes enables the writing of reusable code.
Example
The example needs to be pared down to a manageable size.
Untar the Tab.tar.gz file under tests into tests/Tab. This will allow the
test-all.R script to run.
When setting up a new project the package will download SRAmetadb.sqlite unless you point it to a current location.
SRA files are downloaded if not present. This is time consuming, obviously. The files are available on our computer server storage, and can be copied from there for development.
Basic functionality exits, needs work to generalize to other tools.
RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
RNASeqPipelineR
Streamline the processing of RNASeq data
System requirements
You need the following R packages: data.table GEOquery RSQLite SRAdb
The following command line utilities: SRA Toolkit (from NCBI http://www.ncbi.nlm.nih.gov/books/NBK158900/) ascp (Aspera scp client, distributed with Aspera Connect) RSEM (http://deweylab.biostat.wisc.edu/rsem/) bowtie2 (http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html) BioConductor (http://www.bioconductor.org/) MiTCR (http://mitcr.milaboratory.com/) fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) PEAR (http://sco.h-its.org/exelixis/web/software/pear/) for paired end assembly GEOQuery from BioConductor
Development Notes
Still under development.
Why?
The basic idea behind the package is to held organize and manage the pipeline of processing fastq files, whether they come from data on GEO, or whether they are provided by collaborators.
The package creates a standard directory structure for each project and tracks where files are stored, how they are processed,and generates a report describing what tools are used in the processing.
Output files are annotated and stored in standard locations and convenience functions are provided to construct ExpressionSet or SingleCellAssay objects with full feature and phenotypic (pData) annotations.
When working collaboratively it's important not to duplicate effort. Different people working on the same data set need to ensure that they are working with data that has been processed the same way, and if there are multiple analyses, having that data located and processed in a predictable way and stored in a standard locations becomes enables the writing of reusable code.
Example
The example needs to be pared down to a manageable size.
Untar the Tab.tar.gz file under tests into tests/Tab. This will allow the
test-all.R script to run.
When setting up a new project the package will download SRAmetadb.sqlite unless you point it to a current location.
SRA files are downloaded if not present. This is time consuming, obviously. The files are available on our computer server storage, and can be copied from there for development.
Basic functionality exits, needs work to generalize to other tools.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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