[Bioc 34] NEWS of my BioC packages

I have 7 packages published within the Bioconductor project.

A new package meshes was included in BioC 3.4 release.

ChIPseeker

For ChIPseeker, this release fixed several minor bugs.

GEO data was updated, now ChIPseeker contains 20947 bed file information.

CHANGES IN VERSION 1.9.8
------------------------
 o plotAvgProf/plotAvgProf2 order of panel by names of input tagMatrix List <2016-09-25, Sun>
 o test ENSEMBL ID using '^ENS' instead of '^ENSG' <2016-09-20, Tue>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/41

CHANGES IN VERSION 1.9.7
------------------------
 o unit test <2016-08-16, Tue>

CHANGES IN VERSION 1.9.6
------------------------
 o update vignette <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. <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 <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 <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 <2016-06-14, Tue>

CHANGES IN VERSION 1.9.4
------------------------
 o bug fixed <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 <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 <2016-05-12, Thu>
 o https://github.com/Bioconductor-mirror/ChIPseeker/commit/d5f16b2bc01725e30282c3acb33007ef521a514c

CHANGES IN VERSION 1.9.1
------------------------
 o bug fixed in getNearestFeatureIndicesAndDistances <2016-05-11, Wed>
   + correct metadata in dummy NA feature

clusterProfiler

Thanks to the update of GOSemSim, now simplify method for removing redundent GO terms can be applied to all species that have OrgDb object.

summary for compareClusterResult object was deprecated, user need to use as.data.frame. Several accesor functions including $, [ and [[ were supported as well as head, tail and dim for compareClusterResult object.

browseKEGG function was added, which can open browser and highligh enriched genes in the pathway.

Updates of DOSE also affect clusterProfiler, especially the leading edge analysis was incorporated.

CHANGES IN VERSION 3.1.9
------------------------
 o bug fixed of simplify method for compareCluster object <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 <2016-09-29, Thu>
 o geneID and geneInCategory methods <2016-09-19, Mon>

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

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

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

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

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

CHANGES IN VERSION 3.1.2
------------------------
 o 'by' parameter for GSEA analysis <2016-07-04, Mon>
 o duplicated KEGG path id for KEGG orthology, only use ko <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 <2016-05-20, Fri>
   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/clusterprofiler/zNYHLI6RpJI/1u4XRKfNAQAJ
 o use byte compiler <2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/clusterProfiler/commit/2949fe8db5464c419c9d1665cb24f43c49ac54ec

DOSE

I am glad to release DOSE v3.0, the most important enhancement is now GSEA supports leading edge analysis.

Thanks to the invitation from Alexey Sergishichev, I switch to fgsea in DOSE for calculating enrichment score of GSEA analysis. User can still use my implementation by specifying by="DOSE".

Now enrichMap and cnetplot output igraph object, so that it can be viewed by other software (e.g. networkD3). title parameter is supported in gseaplot.

Several accessor functions, including $, [, and [[ were implemented for enrichResult and gseaResult object. head, tail and dim is also supported. summary method was deprecated, instead user should use as.data.frame to convert the enrichResult or gseaResult object to data.frame.

In additional to DO and NCG, DisGeNET data was incorporated and we can identify disease association by using this annotation.

CHANGES IN VERSION 2.11.12
------------------------
 o deprecate summary method and use as.data.frame instead <2016-09-29, Thu>

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

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

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

CHANGES IN VERSION 2.11.8
------------------------
 o add unit test <2016-08-15, Mon>

CHANGES IN VERSION 2.11.7
------------------------
 o change for meshes packages <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 <2016-08-02, Tue>
 o support DisGeNET enrichment analyses <2016-08-01, Mon>
   + enrichDGN, enrichDGNv, gseDGN
 o update vignettes <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 <2016-07-25, Mon>
 o dim methods for enrichResult and gseaResult <2016-07-22, Fri>
 o $ methods for enrichResult and gseaResult <2016-07-20, Wed>
 o switch from parallel to BiocParallel <2017-07-07, Thu>
 o [, head and tail methods for enrichResult and gseaResult <2016-07-06, Wed>
 o change according to GOSemSim <2016-07-05, Tue>

CHANGES IN VERSION 2.11.4
------------------------
 o 'title' parameter for gseaplot <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' <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 <2016-07-04, Mon>

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

CHANGES IN VERSION 2.11.2
------------------------
 o use byte compiler <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

ggtree

I am very happy that ggtree was published in MEE.

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12628.

In this release, more functionalities were added and of course several bug fixed.

File parsing

read.phyloT for parsing newick format of phyloT output.

read.nhx supports newick file as NHX format allow tree without nhx tags.

Support reading BEAST MCC trees by read.beast function.

tree object support

phylo4d defined in phylobase package is supported, and associated data stored in phylo4d object can be used to annotate the tree directly in ggtree.

Geom

New geoms including geom_strip, geom_range, geom_balance (contributed by Justin Silverman, the author of philr).

geom_cladelabel now supports parsing expression to label clades.

Layout

fan layout is supported, and user can use open_tree function to transform a tree from rectangular or circular to fan layout.

Enhancement and utilities

identify method support annotating trees interactively.

facet_plot supports aligning other plots to phylogenetic trees.

as.polytomy allow collapsing binary tree to polytomy by applying ‘fun’ to selected ‘feature’ (e.g. bootstrap value less than 70).

rotate_tree allow user to rotating circular layout tree.

CHANGES IN VERSION 1.5.17
------------------------
 o read.nhx support newick file <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 <2016-10-11, Tue>
   + https://www.biostars.org/p/210401/#216128
 o fixed aes mapping in geom_strip <2016-10-11, Tue>
 o fixed R check <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 <2016-10-07, Fri>
 o recalculate 'angle' when collapse, expand and rotate clade <2016-10-06, Thu>
   + https://github.com/GuangchuangYu/ggtree/issues/78

CHANGES IN VERSION 1.5.14
------------------------
 o subset tip in geom_tiplab2 <2016-10-05, Wed>
 o add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>
   + https://github.com/hadley/ggplot2/issues/1797
 o unit test for groupOTU and groupClade <2016-09-22, Thu>
 o groupOTU label groups by input group names (when input is a named list) <2016-09-22, Thu>
 o update angle calculation for geom_tiplab <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). <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 <2016-09-06, Tue>
 o more parameters for column names in gheatmap <2016-09-06, Tue>
   + colnames_angle
   + colnames_offset_x
   + colnames_offset_y
   + hjust
 o offset parameter in geom_tiplab and geom_tiplab2 <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 <2016-09-01, Thu>
 o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>

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

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

CHANGES IN VERSION 1.5.9
------------------------
 o update citation info <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 <2016-08-11, Thu>
 o geom_cladelabel support parsing expression <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  <2016-07-27, Wed>
 o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>

CHANGES IN VERSION 1.5.6
------------------------
 o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
   + still needed for building vignette and for processing FASTA file
 o remove dependency of EBImage for building & installing ggtree <2016-07-21, Thu>
   + the package is still needed if user want to annotate tree with image file
 o `%<+%` now works with tbl_df <2016-07-21, Thu>
   + https://github.com/GuangchuangYu/ggtree/issues/66
 o identify method for ggtree <2016-06-28, Tue>
   + see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree
 o geom_balance contributed by Justin Silverman <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 <2016-06-20, Mon>
 o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu>
 o bug fixed if time-scaled tree extend into the BCE. <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 <2016-05-22, Sun>
 o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>
 o bug fixed in collapse <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 <2016-05-18, Wed>
 o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106

CHANGES IN VERSION 1.5.3
------------------------
 o add examples in vignettes <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 <2016-05-12, Thu>
 o rotate_tree and open_tree function <2016-05-12, Thu>
 o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <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 <2016-05-12, Thu>
 o add example of integrate user's data using phylo4d in treeAnnotation vignette <2016-05-11, Wed>
 o add extend, extendto parameter in geom_hilight <2016-05-10, Tue>
 o geom_hilight now supports hilight tips <2016-05-10, Tue>
   + https://github.com/GuangchuangYu/ggtree/issues/53
 o more accurate ylim & angle for circular layout <2016-05-10, Tue>
   + https://github.com/GuangchuangYu/ggtree/issues/40
 o supports phylo4d object <2016-05-10, Tue>
   + https://github.com/GuangchuangYu/ggtree/issues/47

CHANGES IN VERSION 1.5.1
------------------------
 o update vignettes <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 <2016-05-09, Mon>
   + contributed by Justin Silverman <jsilve24@gmail.com>
   + https://github.com/GuangchuangYu/ggtree/pull/57
 o geom_strip for associated taxa <2016-05-09, Mon>
   + https://github.com/GuangchuangYu/ggtree/issues/52

GOSemSim

After 7.5 years in Bioconductor, I bump up the version of GOSemSim to 2.0 for optimization of Wang method and extend GOSemSim to all species that have OrgDb object which can be queried by AnnotationHub.

CHANGES IN VERSION 1.99.4
------------------------
 o fixed NOTE in R check <2016-08-12, Fri>
 o add unit test using testthat <2016-08-11, Thu>

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

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

CHANGES IN VERSION 1.99.1
------------------------
 o update vignette <2016-07-14, Thu>

CHANGES IN VERSION 1.99.0
------------------------
 o support all organisms that have OrgDb object <2016-07-05, Tue>
 o optimize Wang method <2016-07-04, Mon>

meshes

MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.

meshes was newly introduced in this BioC release branch. It supports semantic similarity measurement and enrichment analysis of more than 70 species.

CHANGES IN VERSION 0.99.7
------------------------
 o Depends DOSE <2016-09-29, Thu>
 
CHANGES IN VERSION 0.99.6
------------------------
 o update docs <2016-09-19, Mon>
 
CHANGES IN VERSION 0.99.3
------------------------
 o remove non-ASCII character in vignettes/meshes.bib <2016-08-16, Tue>

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

CHANGES IN VERSION 0.99.1
------------------------
 o R check passed <2016-08-16, Tue>
 
CHANGES IN VERSION 0.99.0
------------------------
 o add vignette <2016-08-11, Thu>
 o enrichMeSH and gseMeSH <2016-08-11, Thu>
   + move from clusterProfiler
 
CHANGES IN VERSION 0.0.1
------------------------
 o geneSim <2016-08-10, Wed>
 o meshSim <2016-08-05, Fri>

ReactomePA

For ReactomePA itself, the change is minor. I only add unit test to this package.

But there are some changes of DOSE also affect this package as it internally use DOSE for enrichment analysis, including leading edge analysis for GSEA and other minor changes.

CHANGES IN VERSION 1.17.4
------------------------
 o unit test <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 <2016-07-06, Wed>
 o 'by' parameter for GSEA analysis <2016-07-04, Mon>

CHANGES IN VERSION 1.17.2
------------------------
 o use byte compiler <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

Citation

Yu G, Wang LG and He QY*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383.

Yu G, Wang L, Han Y and He Q*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609.

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12628.

Yu G, Li F, Qin Y, Bo X*, Wu Y and Wang S*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978.

G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479.

comments powered by Disqus