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work in progress: shifting from Sweave to knitr

paul-shannon authored on 07/04/2020 17:40:05
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+---
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+title: "MotifDb"
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+output:
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+   html_document:
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+      toc: true
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+      toc_float: false
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+vignette: >
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+  %\VignetteIndexEntry{"A collection of PWMs"}
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+  %\VignetteEngine{knitr::knitr}
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+  %\VignetteEncoding{UTF-8}
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+---
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+# Introduction
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+
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+Many kinds of biological activity are regulated by the binding of proteins to their cognate
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+substrates.  Of particular interest is the sequence-specific binding of transcription factors to
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+DNA, often in regulatory regions just upstream of the transcription start site of a gene.  These
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+binding events play a pivotal role in regulating gene expression.  Sequence specificity among
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+closely related binding sites is nearly always incomplete: some variety in the DNA sequence is
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+routinely observed.  For this reason, these inexact binding sequence patterns are commonly described
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+as **motifs**, represented numerically as frequency matrices, and visualized as sequence logos.
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+
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+Despite their importance in current research, there has been until now no single, annotated,
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+comprehensive collection of publicly available motifs. The current package attempts to provide such
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+a collection, offering more than ten thousand annotated matrices from multiple organisms, within the
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+context of the Bioconductor project.  The matrices can be filtered and selected on the basis of
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+their metadata, used with other Bioconductor packages (for instance, seqLogo can be used for for
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+visualization) or easily exported for use with standard software and websites such as those provided
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+by the [MEME Suite](http://meme.sdsc.edu/meme/doc/meme.html).
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+
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+Transcription factor binding sites (TFBS) can only be imperfectly predicted from sequence matching
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+of motif to DNA sequence.  When using MotifDb, please keep in mind that actual and functional TF
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+binding occurs under the influence of many factors:
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+
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+  * Chromatin accessibility
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+  * An appropriate balance of activating and repressing epigenetic influences
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+  * The presence of the the transcription factor protein in adequate numbers
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+  * "DNA shape" to complement or substitute for DNA sequence match
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+  * Cooperativity with other DNA-binding factors, or co-factor interaction
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+
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+Still, motif-matching to DNA sequence plays an important role in identifying gene regulatory events.
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+
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+# Quick Start
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+
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+default:
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+	R -e "rmarkdown::render('MotifDb.Rmd')"
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+	open MotifDb.html