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diff --git a/README b/README index 51161ff..4d22d98 100644 --- a/README +++ b/README @@ -7,6 +7,8 @@ of ChIP-Seq data and has been applied to the organism Tetrahymena thermophila. === Content === +* Overview + * Requirements * Installation @@ -31,6 +33,26 @@ of ChIP-Seq data and has been applied to the organism Tetrahymena thermophila. ================ +* Overview + +Our computational pipeline Rapidly Aanalyze ChIP-Seq data (RACS) can be used +for any genome that has files containing coordinate sequences of interest. +Our pipeline provides a unified tool to perform comprehensive ChIP-Seq data +analysis. +For instance, with RACS users obtain the co-ordinates of ChIP peaks as well as +information regarding their relative enrichment across the genome, i.e. number +of significant peaks found with genic versus non-genic regions. +RACS is a versatile computational pipeline suitable to analyze ChIP-Seq data +generated using any model organism. + + +This pipeline is open source under the MIT license, and researchers are welcome +to use it. +We will appreciate if users can let us know if they found bugs or could provide +feedback about its use and experience using RACS. +Please cite our paper (CITE_RACS) when ever you are using RACS. + + * Requirements @@ -51,10 +73,17 @@ Additionally we provide other subdirectories containing the following: also we included one monitoring tool to observe the memory/RAMdisk usage while RACS is running - "datasets": examples of the data used to test and run our pipeline -This pipeline is open source under the MIT license, and researchers are welcome to use it. -We will appreciate if users can let us know if they found bugs or could provide feedback about -its use and experience using RACS. -Please cite our paper (CITE_RACS) when ever you are using RACS. +- Other dependencies: +Our core scripts do not require any additional R packages; however, the +comparison tools, depending on what format the data to compare with is given, +might use some spreadsheet reader package. +For instance, we have included one named \texttt{xlsx} which allows to read +proprietary spreadsheet formats. +To aid the process of identifying and installing the auxiliary R packages +needed by these tools, we included an R script called "setup.R", that can be +run from the command line to check and install these dependencies (more details +are presented in the Examples section). +