Enrichmentbrowser rmd

[Rohit-Satyam]

This Repo now contains RMD files in Vignette folder.

[lgeistlinger]

The references in-text as well as in the References section are not properly formatted, compare to the PDF version.

[lgeistlinger]

echo = FALSE should translate to message = FALSE to prevent printing of package startup messages

[lgeistlinger]

Instances such as

DAVID (https://david.ncifcrf.gov/) and Pathway Studio (https://www.pathwaystudio.com/) (Section 12.1)

and

GO (http://www.geneontology.org/) and KEGG (http://www.genome.jp/kegg) (Section 12.3)

could be simply links instead of showing the URL in brackets.

[lgeistlinger]

In section 12.4 a reference

@ref(#sec:ora)

seem to not render.

[lgeistlinger]

Thanks @jwokaty - sure we can add Rohit as a contributor. Please insert as contributor after Mirko Signorelli and before Marcel Ramos. Thanks for your efforts!

[jwokaty]

Hi @lgeistlinger, I wanted to you to review the PR. I also want to mention three changes in particular and ask if you wanted any changes to be made.

• the appendix is now numbered rather than alphabetical
• the last paragraph of the introduction uses the section number as a link rather than the name of the section
• the references section has improved formatting, but uses initials rather than the full names

[Rohit-Satyam]

Hi guys!! I was wondering if this PR review is complete and ready to merge?

[lgeistlinger]

Hi @Rohit-Satyam @jwokaty: sorry for the delay. Except for the references everything looks good. Can the references be fixed? See eg the SingleR package or the MouseGastrulationData package for an acceptable formatting of references within Bioc RMD vignettes. Thanks!

[Rohit-Satyam]

Hi I wanted to understand if the references needs to be formatted in terms of CSL styling or the intext citation shouldn't be numeric? I was going through the SingleR and MouseGastrulationData and I didn't see any custom formatting or styling file so I am assuming you want .csl file to be removed? Is it so?

Edit1: I observed that he .bib file has many missing fields so I am revising it as well. I also observed that the following publication in refs.bib has not been cited in text. Where do you want this ?

@article{kim2013,
	title = {Stouffer{\textquoteright}s Test in a Large Scale Simultaneous Hypothesis Testing},
	author = {Kim, Sang Cheol and Lee, Seul Ji and Lee, Won Jun and Yum, Young Na and Kim, Joo Hwan and Sohn, Soojung and Park, Jeong Hill and Lee, Jeongmi and Lim, Johan and Kwon, Sung Won},
	editor = {Guo, Wenge},
	year = {2013},
	month = {05},
	date = {2013-05-14},
	journal = {PLoS ONE},
	pages = {e63290},
	volume = {8},
	number = {5},
	doi = {10.1371/journal.pone.0063290},
	url = {http://dx.doi.org/10.1371/journal.pone.0063290},
	langid = {en}
}

[lgeistlinger]

Hi @Rohit-Satyam sorry for the delay. The Kim 2013 reference can be removed. It has been used in older versions of the package, but is not used anymore. I would prefer to keep a similar citation style as currently used (ie numeric intext citations), but it does not need to be exactly BMC Bioinformatics style if this causes problems.

[Rohit-Satyam]

Hi The requested changes have been made. Kindly check the vignette now.

[lgeistlinger]

Great, thank you!