Blog Archives

functional enrichment for GTEx paper

August 12, 2015
By
functional enrichment for GTEx paper

The ENCODE consortium has recently published a great paper on Gene Expression from the GTEx dataset. A criticism raised on pubpeer is that the gene ontology enrichment analysis was done with DAVID which has not been updated in the last five years. The result is shown below: Read More: 1771 Words Totally

Read more »

parsing BED coordinates

August 6, 2015
By
parsing BED coordinates

In supplemental file of ChIPseeker paper. I compare distances to TSS reported by several ChIP annotation software, including ChIPseeker, ChIPpeakAnno, HOMER and PeakAnalyzer. Although I found that the chromStart positions in HOMER output have a +1 shift compare to other software, I did not realize this issue since all other software are consistent. Read More: 1102 Words...

Read more »

[ggtree] annotate phylogenetic tree with local images

August 1, 2015
By
[ggtree] annotate phylogenetic tree with local images

In ggtree, we provide a function annotation_image for annotating phylogenetic tree with images. To demonstrate the usage, I created a tree view from a random tree as shown below: Read More: 973 Words Totally

Read more »

upsetplot in ChIPseeker

July 28, 2015
By
upsetplot in ChIPseeker

ChIPseeker is an R package for ChIP peak annotation, comparison and visualization. We have implemented several visualization methods, including vennpie that was designed for viewing annotation overlap as shown below: Read More: 457 Words Totally

Read more »

[paper published] ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

July 13, 2015
By
[paper published] ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

My R/Bioconductor package, ChIPseeker, published in Bioinformatics. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization Read More: 992 Words Totally

Read more »

flip and rotate branches in ggtree

June 30, 2015
By
flip and rotate branches in ggtree

flip function is a feature request from ggtree user. It accepts a tree view and two node numbers and exchange the positions of the selected clades. ?View Code RSPLUS1 Read More: 159 Words Totally

Read more »

dotplot for enrichment result

June 22, 2015
By
dotplot for enrichment result

This is a feature request from clusterProfiler user. It's similar to what I implemented in clusterProfiler for comparing biological themes. For comparing different enrichment results, the x-axis represent different gene clusters while for a single enrichment result, the x-axis can be gene count or gene ratio. This is actually similar to traditional barplot, with dot position as bar height...

Read more »

ggtree with funny fonts

June 12, 2015
By
ggtree with funny fonts

showtext is a neat solution to use various types of fonts in R graphs and make it easy to use funny fonts. With showtext, we can draw phylogenetic tree with different types of fonts even with symbolic/icon fonts. Read More: 638 Words Totally

Read more »

BMC favors source code plagiarism

May 27, 2015
By
BMC favors source code plagiarism

I found source code plagiarism a year ago and reported this case to BMC Systems Biology: I listed source code of many functions that are exactly copied from GOSemSim with only function name changed in my email. The detail of source code plagiarism can also be found at Proper use of GOSemSim. Read More: 9738...

Read more »

use clusterProfiler as an universal enrichment analysis tool

May 11, 2015
By
use clusterProfiler as an universal enrichment analysis tool

clusterProfiler supports enrichment analysis of both hypergeometric test and gene set enrichment analysis. It internally support Gene Ontology analysis of about 20 species, Kyoto Encyclopedia of Genes and Genomes (KEGG) with all species that have annotation available in KEGG database, DAVID annotation, Disease Ontology and Network of Cancer Genes (via DOSE for human) and Reactome Pathway (via ReactomePA for...

Read more »

Sponsors

Mango solutions



RStudio homepage



Zero Inflated Models and Generalized Linear Mixed Models with R

Quantide: statistical consulting and training



http://www.eoda.de









ODSC

CRC R books series











Contact us if you wish to help support R-bloggers, and place your banner here.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)