<p><div><div><div><div data-width="100" data-show-faces="false" data-send="true" data-layout="button_count" data-height="21" data-href="https://www.r-bloggers.com/bioc-34-news-of-my-bioc-packages/"></div></div><div><a data-url="https://www.r-bloggers.com/bioc-34-news-of-my-bioc-packages/" data-counturl="https://www.r-bloggers.com/bioc-34-news-of-my-bioc-packages/" data-count="horizontal" data-text="[Bioc 34] NEWS of my BioC packages" class="twitter-share-button" data-via="rbloggers" href="https://twitter.com/share"></a></div><div></div></div><div></div></div>
<div>
(This article was first published on <strong><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages"> R on Guangchuang YU</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p>I have 7 packages published within the <code>Bioconductor</code> project.</p>
<ul>
<li><a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/ChIPseeker">ChIPseeker</a></li>
<li><a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/clusterProfiler">clusterProfiler</a></li>
<li><a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/DOSE">DOSE</a></li>
<li><a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/ggtree">ggtree</a></li>
<li><a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/GOSemSim">GOSemSim</a></li>
<li><a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/meshes">meshes</a></li>
<li><a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/ReactomePA">ReactomePA</a></li>
</ul>
<p>A new package <a target="_blank" rel="nofollow" href="http://guangchuangyu.github.io/meshes">meshes</a> was included in BioC 3.4 release.</p>
<h2>ChIPseeker</h2>
<p>For <code>ChIPseeker</code>, this release fixed several minor bugs.</p>
<p>GEO data was updated, now <code>ChIPseeker</code> contains <code>20947</code> bed file information.</p>
<pre><code>CHANGES IN VERSION 1.9.8
------------------------
 o plotAvgProf/plotAvgProf2 order of panel by names of input tagMatrix List &lt;2016-09-25, Sun>
 o test ENSEMBL ID using '^ENS' instead of '^ENSG' &lt;2016-09-20, Tue>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/41

CHANGES IN VERSION 1.9.7
------------------------
 o unit test &lt;2016-08-16, Tue>

CHANGES IN VERSION 1.9.6
------------------------
 o update vignette &lt;2016-08-16, Tue>

CHANGES IN VERSION 1.9.5
------------------------
 o when TxDb doesn't have gene_id information, converting gene ID (ensembl/entrez and symbol) will be omitted instead of throw error. &lt;2016-08-02, Tue>
   + https://www.biostars.org/p/204142
 o bug fixed if testing targetPeak is a list of GRanges objects in enrichPeakOverlap function &lt;2016-07-20, Wed>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/37
   + https://github.com/GuangchuangYu/ChIPseeker/issues/36
 o fixed typo in determine gene ID type &lt;2016-06-21, Tue>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/28#issuecomment-227212519
 o move upsetplot generics to DOSE and import from DOSE to prevent function name conflict &lt;2016-06-14, Tue>

CHANGES IN VERSION 1.9.4
------------------------
 o bug fixed &lt;2016-06-08, Wed>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/17#issuecomment-224407402
   + https://github.com/GuangchuangYu/ChIPseeker/pull/24/files

CHANGES IN VERSION 1.9.3
------------------------
 o use byte compiler &lt;2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/ChIPseeker/commit/f1ada57b9c66a1a44355bbbbdaf5b0a88e10cf7d

CHANGES IN VERSION 1.9.2
------------------------
 o name tagMatrix in plotAvgProf automatically if missing &lt;2016-05-12, Thu>
 o https://github.com/Bioconductor-mirror/ChIPseeker/commit/d5f16b2bc01725e30282c3acb33007ef521a514c

CHANGES IN VERSION 1.9.1
------------------------
 o bug fixed in getNearestFeatureIndicesAndDistances &lt;2016-05-11, Wed>
   + correct metadata in dummy NA feature
</code></pre>
<h2>clusterProfiler</h2>
<p>Thanks to the update of <code>GOSemSim</code>, now <code>simplify</code> method for removing redundent GO terms can be applied to all species that have <code>OrgDb</code> object.</p>
<p><code>summary</code> for <code>compareClusterResult</code> object was deprecated, user need to use <code>as.data.frame</code>. Several accesor functions including <code>$</code>, <code>[</code> and <code>[[</code> were supported as well as <code>head</code>, <code>tail</code> and <code>dim</code> for <code>compareClusterResult</code> object.</p>
<p><code>browseKEGG</code> function was added, which can open <code>browser</code> and highligh enriched genes in the pathway.</p>
<p>Updates of <code>DOSE</code> also affect <code>clusterProfiler</code>, especially the leading edge analysis was incorporated.</p>
<pre><code>CHANGES IN VERSION 3.1.9
------------------------
 o bug fixed of simplify method for compareCluster object &lt;2016-08-17, Mon>
   + use semData parameter according to the change of GOSemSim

CHANGES IN VERSION 3.1.8
------------------------
 o as.data.frame method for compareClusterResult &lt;2016-09-29, Thu>
 o geneID and geneInCategory methods &lt;2016-09-19, Mon>

CHANGES IN VERSION 3.1.7
------------------------
 o [, [[, head, tail, dim methods for compareClusterResult &lt;2016-08-28, Sun>
 o fixed R-devel check &lt;2016-08-16, Tue>

CHANGES IN VERSION 3.1.6
------------------------
 o update vignette &lt;2016-08-16, Tue>
 o browseKEGG &lt;2016-08-15, Mon>
 o unit test &lt;2016-08-15, Mon>

CHANGES IN VERSION 3.1.5
------------------------
 o move enrichMeSH &amp; gseMeSH to meshes &lt;2016-08-11, Thu>

CHANGES IN VERSION 3.1.4
------------------------
 o MeSH term enrichment analysis (enrichMeSH and gseMeSH) &lt;2016-07-28, Thu>

CHANGES IN VERSION 3.1.3
------------------------
 o export download_KEGG &lt;2016-07-25, Mon>
 o according to the changes of GOSemSim and DOSE &lt;2016-07-05, Tue>

CHANGES IN VERSION 3.1.2
------------------------
 o 'by' parameter for GSEA analysis &lt;2016-07-04, Mon>
 o duplicated KEGG path id for KEGG orthology, only use ko &lt;2016-06-28, Tue>
   + e.g. map00010 and ko00010
   + http://www.kegg.jp/dbget-bin/www_bget?ko+ko00010
   + http://www.kegg.jp/dbget-bin/www_bget?ko+map00010

CHANGES IN VERSION 3.1.1
------------------------
 o getGOLevel and dropGO support using a vector of GO level &lt;2016-05-20, Fri>
   + https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/clusterprofiler/zNYHLI6RpJI/1u4XRKfNAQAJ
 o use byte compiler &lt;2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/clusterProfiler/commit/2949fe8db5464c419c9d1665cb24f43c49ac54ec
</code></pre>
<h2>DOSE</h2>
<p>I am glad to release <code>DOSE</code> v3.0, the most important enhancement is now GSEA supports <a target="_blank" rel="nofollow" href="https://guangchuangyu.github.io/2016/07/leading-edge-analysis/">leading edge analysis</a>.</p>
<p>Thanks to the invitation from Alexey Sergishichev, I switch to <code>fgsea</code> in <code>DOSE</code> for calculating enrichment score of GSEA analysis. User can still use my implementation by specifying <code>by=&quot;DOSE&quot;</code>.</p>
<p>Now <code>enrichMap</code> and <code>cnetplot</code> output <code>igraph</code> object, so that it can be viewed by other software (e.g. networkD3). <code>title</code> parameter is supported in <code>gseaplot</code>.</p>
<p>Several accessor functions, including <code>$</code>, <code>[</code>, and <code>[[</code> were implemented for <code>enrichResult</code> and <code>gseaResult</code> object. <code>head</code>, <code>tail</code> and <code>dim</code> is also supported. <code>summary</code> method was deprecated, instead user should use <code>as.data.frame</code> to convert the <code>enrichResult</code> or <code>gseaResult</code> object to <code>data.frame</code>.</p>
<p>In additional to <code>DO</code> and <code>NCG</code>, <code>DisGeNET</code> data was incorporated and we can identify disease association by using this annotation.</p>
<pre><code>CHANGES IN VERSION 2.11.12
------------------------
 o deprecate summary method and use as.data.frame instead &lt;2016-09-29, Thu>

CHANGES IN VERSION 2.11.11
------------------------
 o export geneID and geneInCategory &lt;2016-09-19, Mon>

CHANGES IN VERSION 2.11.10
------------------------
 o geneID and geneInCategory accessor functions &lt;2016-09-19, Mon>

CHANGES IN VERSION 2.11.9
------------------------
 o enrichMap works with result contains only one term &lt;2016-08-15, Wed>
   + https://github.com/GuangchuangYu/DOSE/issues/15
 o build_Anno now works with tibble &lt;2016-08-18, Tue>

CHANGES IN VERSION 2.11.8
------------------------
 o add unit test &lt;2016-08-15, Mon>

CHANGES IN VERSION 2.11.7
------------------------
 o change for meshes packages &lt;2016-08-11, Thu>

CHANGES IN VERSION 2.11.6
------------------------
 o user can use options(DOSE_workers = x) to set using x cores for GSEA analysis &lt;2016-08-02, Tue>
 o support DisGeNET enrichment analyses &lt;2016-08-01, Mon>
   + enrichDGN, enrichDGNv, gseDGN
 o update vignettes &lt;2016-07-29, Fri>

CHANGES IN VERSION 2.11.5
------------------------
 o enrichMap now output igraph object that can be viewed using other software like networkD3 &lt;2016-07-25, Mon>
 o dim methods for enrichResult and gseaResult &lt;2016-07-22, Fri>
 o $ methods for enrichResult and gseaResult &lt;2016-07-20, Wed>
 o switch from parallel to BiocParallel &lt;2017-07-07, Thu>
 o [, head and tail methods for enrichResult and gseaResult &lt;2016-07-06, Wed>
 o change according to GOSemSim &lt;2016-07-05, Tue>

CHANGES IN VERSION 2.11.4
------------------------
 o 'title' parameter for gseaplot &lt;2016-07-04, Mon>
   + contributed by https://github.com/pedrostrusso
   + https://github.com/GuangchuangYu/DOSE/pull/13
 o 'by' parameter in GSEA_internal, by default by = 'fgsea' &lt;2016-07-04, Mon>
   + by = 'fgsea', use GSEA algorithm implemented in fgsea
   + by = 'DOSE', use GSEA algorithm implemented in DOSE
 o leading edge analysis for GSEA &lt;2016-07-04, Mon>

CHANGES IN VERSION 2.11.3
------------------------
 o output igraph object in cnetplot &lt;2016-06-21, Tue>
 o upsetplot generics &lt;2016-06-14, Tue>
 o [[ methods for enrichResult and gseaResult for accessing gene set &lt;2016-06-14, Tue>

CHANGES IN VERSION 2.11.2
------------------------
 o use byte compiler &lt;2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/DOSE/commit/6c508c6a6816f465bb372f30f4ab99c839d81767

CHANGES IN VERSION 2.11.1
------------------------
 o https://github.com/Bioconductor-mirror/DOSE/commit/7e87d01e671ce1b5fbe974c06b796b1a2970f11c
</code></pre>
<h2>ggtree</h2>
<p>I am very happy that <code>ggtree</code> was published in <code>MEE</code>.</p>
<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. <a target="_blank" rel="nofollow" href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a>. <strong><em>Methods in Ecology and Evolution</em></strong>. <a target="_blank" rel="nofollow" href="http://dx.doi.org/10.1111/2041-210X.12628"><code>doi:10.1111/2041-210X.12628</code></a>.</p>
<p>In this release, more functionalities were added and of course several bug fixed.</p>
<h3>File parsing</h3>
<p><code>read.phyloT</code> for parsing newick format of <a target="_blank" rel="nofollow" href="https://www.biostars.org/p/210401/#216128">phyloT output</a>.</p>
<p><code>read.nhx</code> supports newick file as NHX format allow tree without <code>nhx</code> tags.</p>
<p>Support reading BEAST MCC trees by <code>read.beast</code> function.</p>
<h3>tree object support</h3>
<p><code>phylo4d</code> defined in <code>phylobase</code> package is supported, and associated data stored in <code>phylo4d</code> object can be used to annotate the tree directly in <code>ggtree</code>.</p>
<h3>Geom</h3>
<p>New geoms including <code>geom_strip</code>, <code>geom_range</code>, <code>geom_balance</code> (contributed by Justin Silverman, the author of <a target="_blank" rel="nofollow" href="https://www.bioconductor.org/packages/philr">philr</a>)</p>
<p><code>geom_cladelabel</code> now supports parsing expression to label clades.</p>
<h3>Layout</h3>
<p><code>fan</code> layout is supported, and user can use <code>open_tree</code> function to transform a tree from <code>rectangular</code> or <code>circular</code> to <code>fan</code> layout.</p>
<h3>Enhancement and utilities</h3>
<p><a target="_blank" rel="nofollow" href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify</a> method support annotating trees interactively.</p>
<p><code>facet_plot</code> supports aligning other plots to phylogenetic trees.</p>
<blockquote class="twitter-tweet"><p dir="ltr" lang="en">associate tree with different type of data by <a target="_blank" rel="nofollow" href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> <a target="_blank" rel="nofollow" href="https://t.co/6w755VWytZ">https://t.co/6w755VWytZ</a> <a target="_blank" rel="nofollow" href="https://t.co/K8WViEi13E">pic.twitter.com/K8WViEi13E</a></p>
<p>— Guangchuang Yu (@guangchuangyu) <a target="_blank" rel="nofollow" href="https://twitter.com/guangchuangyu/status/773359054924095488">September 7, 2016</a></p></blockquote>
<p></p>
<p><code>as.polytomy</code> allow collapsing binary tree to polytomy by applying ‘fun’ to selected ‘feature’ (e.g. bootstrap value less than 70).</p>
<p><code>rotate_tree</code> allow user to rotating <code>circular</code> layout tree.</p>
<pre><code>CHANGES IN VERSION 1.5.17
------------------------
 o read.nhx support newick file &lt;2016-10-17, Mon>
   + https://github.com/GuangchuangYu/ggtree/issues/79

CHANGES IN VERSION 1.5.16
------------------------
 o read.phyloT for parsing newick format of phyloT output &lt;2016-10-11, Tue>
   + https://www.biostars.org/p/210401/#216128
 o fixed aes mapping in geom_strip &lt;2016-10-11, Tue>
 o fixed R check &lt;2016-10-10, Mon>
   + check.aes parameter is not available in release version of ggplot2 yet

CHANGES IN VERSION 1.5.15
------------------------
 o check.aes for layers defined in ggtree &lt;2016-10-07, Fri>
 o recalculate 'angle' when collapse, expand and rotate clade &lt;2016-10-06, Thu>
   + https://github.com/GuangchuangYu/ggtree/issues/78

CHANGES IN VERSION 1.5.14
------------------------
 o subset tip in geom_tiplab2 &lt;2016-10-05, Wed>
 o add `compute_group` according to ggplot (v2.1.0) &lt;2016-09-29, Thu>
   + https://github.com/hadley/ggplot2/issues/1797
 o unit test for groupOTU and groupClade &lt;2016-09-22, Thu>
 o groupOTU label groups by input group names (when input is a named list) &lt;2016-09-22, Thu>
 o update angle calculation for geom_tiplab &lt;2016-09-13, Thu>
 o as.polytomy to collapse binary tree to polytomy by applying 'fun' to selected 'feature' (e.g. bootstrap value less than 70). &lt;2016-09-13, Tue>
   + currently only phylo object supported.
   + add test for as.polytomy

CHANGES IN VERSION 1.5.13
------------------------
 o facet_plot for plotting data with tree &lt;2016-09-06, Tue>
 o more parameters for column names in gheatmap &lt;2016-09-06, Tue>
   + colnames_angle
   + colnames_offset_x
   + colnames_offset_y
   + hjust
 o offset parameter in geom_tiplab and geom_tiplab2 &lt;2016-09-05, Mon>

CHANGES IN VERSION 1.5.12
------------------------
 o use data in all layers instead of the base layer for coordination calculation in subview &lt;2016-09-01, Thu>
 o bug fixed in subview, width &amp; height should be width/2 &amp; height/2 &lt;2016-09-01, Thu>

CHANGES IN VERSION 1.5.11
------------------------
 o gheatmap works with matrix &lt;2016-08-28, Sun>
   + https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/2YLvXHMJJ6U/c4zS7yfGCAAJ
 o support parsing expression in geom_strip &lt;2016-08-18, Thu>
 o bug fixed in geom_tiplab &lt;2016-08-17, Wed>
   + https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
 o update citation info, add doi. &lt;2016-08-16, Tue>

CHANGES IN VERSION 1.5.10
------------------------
 o fixed issue #72 for label of geom_treescale not displayed &lt;2016-08-16, Tue>
   + https://github.com/GuangchuangYu/ggtree/issues/72

CHANGES IN VERSION 1.5.9
------------------------
 o update citation info &lt;2016-08-12, Fri>

CHANGES IN VERSION 1.5.8
------------------------
 o add color parameter in geom_cladelabel, color should be of length 1 or 2 &lt;2016-08-11, Thu>
 o geom_cladelabel support parsing expression &lt;2016-08-11, Thu>

CHANGES IN VERSION 1.5.7
------------------------
 o geom_strip can accept taxa name as input but labeling strip will not supported.
   To support labeling strip, user need to input node id  &lt;2016-07-27, Wed>
 o nodeid function for converting node label(s) to node id(s) &lt;2016-07-27, Wed>

CHANGES IN VERSION 1.5.6
------------------------
 o remove dependency of Biostring for installing ggtree &lt;2016-07-21, Thu>
   + still needed for building vignette and for processing FASTA file
 o remove dependency of EBImage for building &amp; installing ggtree &lt;2016-07-21, Thu>
   + the package is still needed if user want to annotate tree with image file
 o `%&lt;+%` now works with tbl_df &lt;2016-07-21, Thu>
   + https://github.com/GuangchuangYu/ggtree/issues/66
 o identify method for ggtree &lt;2016-06-28, Tue>
   + see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree
 o geom_balance contributed by Justin Silverman &lt;2016-06-22, Wed>
   + see https://github.com/GuangchuangYu/ggtree/pull/64

CHANGES IN VERSION 1.5.5
------------------------
 o update geom_tiplab2 according to angle change introduced by open_tree &lt;2016-06-20, Mon>
 o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed &lt;2016-06-02-Thu>
 o bug fixed if time-scaled tree extend into the BCE. &lt;2016-06-02, Thu>
   + as.Date won't work for BCE time.
   + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).

CHANGES IN VERSION 1.5.4
------------------------
 o reroot method for raxml object &lt;2016-05-22, Sun>
 o bug fixed in scaleClade, now y positions are (hopefully) always correct. &lt;2016-05-20, Fri>
 o bug fixed in collapse &lt;2016-05-20, Fri>
   + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
 o use byte compiler &lt;2016-05-18, Wed>
 o change any(is.na()) to anyNA() which is more efficient &lt;2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106

CHANGES IN VERSION 1.5.3
------------------------
 o add examples in vignettes &lt;2016-05-13, Fri>
   + add fan layout example in treeVisualization vignette
   + add open_tree and rotate_tree example in treeManipulation vignette
 o add angle in ggtree function, fan layout supported &lt;2016-05-12, Thu>
 o rotate_tree and open_tree function &lt;2016-05-12, Thu>
 o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function &lt;2016-05-12, Thu>
 o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5

CHANGES IN VERSION 1.5.2
------------------------
 o add multiplot in ggtreeUtilities vignette &lt;2016-05-12, Thu>
 o add example of integrate user's data using phylo4d in treeAnnotation vignette &lt;2016-05-11, Wed>
 o add extend, extendto parameter in geom_hilight &lt;2016-05-10, Tue>
 o geom_hilight now supports hilight tips &lt;2016-05-10, Tue>
   + https://github.com/GuangchuangYu/ggtree/issues/53
 o more accurate ylim &amp; angle for circular layout &lt;2016-05-10, Tue>
   + https://github.com/GuangchuangYu/ggtree/issues/40
 o supports phylo4d object &lt;2016-05-10, Tue>
   + https://github.com/GuangchuangYu/ggtree/issues/47

CHANGES IN VERSION 1.5.1
------------------------
 o update vignettes &lt;2016-05-10, Tue>
   + add geom_range example in treeImport
   + add geom_strip and geom_taxalink example in treeAnnotation
   + add ggtreeUtilities vignette
 o gheatmap now works with data.frame of only one column &lt;2016-05-09, Mon>
   + contributed by Justin Silverman &lt;jsilve24@gmail.com>
   + https://github.com/GuangchuangYu/ggtree/pull/57
 o geom_strip for associated taxa &lt;2016-05-09, Mon>
   + https://github.com/GuangchuangYu/ggtree/issues/52
</code></pre>
<h2>GOSemSim</h2>
<p>After 7.5 years in Bioconductor, I bump up the version of <code>GOSemSim</code> to 2.0 for optimization of <code>Wang</code> method and extend <code>GOSemSim</code> to all species that have <code>OrgDb</code> object which can be queried by <code>AnnotationHub</code>.</p>
<pre><code>CHANGES IN VERSION 1.99.4
------------------------
 o fixed NOTE in R check &lt;2016-08-12, Fri>
 o add unit test using testthat &lt;2016-08-11, Thu>

CHANGES IN VERSION 1.99.3
------------------------
 o changes to satisfy meshes package &lt;2016-08-05, Fri>

CHANGES IN VERSION 1.99.2
------------------------
 o fixed Rcpp issue &lt;2016-07-19, Tue>
   + https://github.com/GuangchuangYu/GOSemSim/issues/6

CHANGES IN VERSION 1.99.1
------------------------
 o update vignette &lt;2016-07-14, Thu>

CHANGES IN VERSION 1.99.0
------------------------
 o support all organisms that have OrgDb object &lt;2016-07-05, Tue>
 o optimize Wang method &lt;2016-07-04, Mon>
</code></pre>
<h2>meshes</h2>
<blockquote>
<p>MeSH (Medical Subject Headings) is the NLM controlled vocabulary<br>
used to manually index articles for MEDLINE/PubMed. MeSH terms were<br>
associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH.<br>
This association is fundamental for enrichment and semantic analyses.<br>
meshes supports enrichment analysis (over-representation and gene set<br>
enrichment analysis) of gene list or whole expression profile.<br>
The semantic comparisons of MeSH terms provide quantitative ways to compute<br>
similarities between genes and gene groups. meshes implemented five methods<br>
proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports<br>
more than 70 species.</p>
</blockquote>
<p><code>meshes</code> was newly introduced in this BioC release branch. It supports semantic similarity measurement and enrichment analysis of more than 70 species.</p>
<pre><code>CHANGES IN VERSION 0.99.7
------------------------
 o Depends DOSE &lt;2016-09-29, Thu>
 
CHANGES IN VERSION 0.99.6
------------------------
 o update docs &lt;2016-09-19, Mon>
 
CHANGES IN VERSION 0.99.3
------------------------
 o remove non-ASCII character in vignettes/meshes.bib &lt;2016-08-16, Tue>

CHANGES IN VERSION 0.99.2
------------------------
 o all exported functions have runnable examples required by BiocCheck &lt;2016-08-16, Tue>

CHANGES IN VERSION 0.99.1
------------------------
 o R check passed &lt;2016-08-16, Tue>
 
CHANGES IN VERSION 0.99.0
------------------------
 o add vignette &lt;2016-08-11, Thu>
 o enrichMeSH and gseMeSH &lt;2016-08-11, Thu>
   + move from clusterProfiler
 
CHANGES IN VERSION 0.0.1
------------------------
 o geneSim &lt;2016-08-10, Wed>
 o meshSim &lt;2016-08-05, Fri>
</code></pre>
<h2>ReactomePA</h2>
<p>For <code>ReactomePA</code> itself, the change is minor. I only add unit test to this package.</p>
<p>But there are some changes of <code>DOSE</code> also affect this package as it internally use <code>DOSE</code> for enrichment analysis, including leading edge analysis for GSEA and other minor changes.</p>
<pre><code>CHANGES IN VERSION 1.17.4
------------------------
 o unit test &lt;2016-08-15, Mon>
 
CHANGES IN VERSION 1.17.3
------------------------
 o move getDb from GOSemSim (no longer need this function) to ReactomePA and remove dependency of GOSemSim &lt;2016-07-06, Wed>
 o 'by' parameter for GSEA analysis &lt;2016-07-04, Mon>

CHANGES IN VERSION 1.17.2
------------------------
 o use byte compiler &lt;2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/ReactomePA/commit/6ce32c8e03e1b252662a07901cce022fab038086

CHANGES IN VERSION 1.17.1
------------------------
 o https://github.com/Bioconductor-mirror/ReactomePA/commit/5d150f5fe545cfa3983872bf5485af1b9ba3129d
</code></pre>
<h2>Citation</h2>
<p><strong><em>Yu G</em></strong>, Wang LG and He QY<sup>*</sup>. <a target="_blank" rel="nofollow" href="http://bioinformatics.oxfordjournals.org/content/31/14/2382">ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization</a>. <strong><em>Bioinformatics</em></strong> 2015, 31(14):2382-2383.</p>
<p>
<div data-badge-popover="right" data-altmetric-id="3781087" data-badge-type="donut"></div>

<p><strong><em>Yu G</em></strong>, Wang L, Han Y and He Q<sup>*</sup>. <a target="_blank" rel="nofollow" href="http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118">clusterProfiler: an R package for comparing biological themes among gene clusters</a>. <strong><em>OMICS: A Journal of Integrative Biology</em></strong>. 2012, 16(5):284-287.</p>
<p>
<div data-badge-popover="right" data-altmetric-id="681089" data-badge-type="donut"></div>

<p><strong><em>G Yu</em></strong>, LG Wang, GR Yan, QY He. <a target="_blank" rel="nofollow" href="http://bioinformatics.oxfordjournals.org/content/31/4/608">DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis</a>. <strong><em>Bioinformatics</em></strong> 2015, 31(4):608-609.</p>
<p>
<div data-badge-popover="right" data-altmetric-id="2788597" data-badge-type="donut"></div>

<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. <a target="_blank" rel="nofollow" href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a>. <strong><em>Methods in Ecology and Evolution</em></strong>. <a target="_blank" rel="nofollow" href="http://dx.doi.org/10.1111/2041-210X.12628"><code>doi:10.1111/2041-210X.12628</code></a>.</p>
<p></p>
<div data-badge-popover="right" data-doi="10.1111/2041-210X.12628" data-badge-type="donut"></div>

<p><strong>Yu G</strong><sup>†</sup>, Li F<sup>†</sup>, Qin Y, Bo X<sup>*</sup>, Wu Y and Wang S<sup>*</sup>. <a target="_blank" rel="nofollow" href="http://bioinformatics.oxfordjournals.org/content/26/7/976">GOSemSim: an R package for measuring semantic similarity among GO terms and gene products</a>. <strong><em>Bioinformatics</em></strong>. 2010, 26(7):976-978.</p>
<p></p>
<div data-badge-popover="right" data-altmetric-id="100979" data-badge-type="donut"></div>

<p><strong><em>G Yu</em></strong>, QY He<sup>*</sup>. <a target="_blank" rel="nofollow" href="http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E#!divAbstract">ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization</a>. <strong><em>Molecular BioSystems</em></strong> 2016, 12(2):477-479.</p>
<p>
<div data-badge-popover="right" data-altmetric-id="4796667" data-badge-type="donut"></div>
<p><div><div><div><div data-width="55" data-show-faces="false" data-send="true" data-layout="box_count" data-height="62" data-href="https://www.r-bloggers.com/bioc-34-news-of-my-bioc-packages/"></div></div><div><a data-url="https://www.r-bloggers.com/bioc-34-news-of-my-bioc-packages/" data-counturl="https://www.r-bloggers.com/bioc-34-news-of-my-bioc-packages/" data-count="vertical" data-text="[Bioc 34] NEWS of my BioC packages" class="twitter-share-button" data-via="rbloggers" href="https://twitter.com/share"></a></div><div></div></div><div></div></div>
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