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hvaret committed Jun 13, 2017
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -2,7 +2,7 @@ Package: SARTools
Type: Package
Title: Statistical Analysis of RNA-Seq Tools
Version: 1.5.0
Date: 2017-06-02
Date: 2017-06-13
Author: Marie-Agnes Dillies and Hugo Varet
Maintainer: Hugo Varet <[email protected]>
Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable
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130 changes: 130 additions & 0 deletions inst/medecine-sciences.csl
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<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" default-locale="en-US">
<info>
<title>médecine/sciences</title>
<id>http://www.zotero.org/styles/medecine-sciences</id>
<link href="http://www.zotero.org/styles/medecine-sciences" rel="self"/>
<link href="http://www.zotero.org/styles/plos" rel="template"/>
<link href="http://www.medecinesciences.org" rel="documentation"/>
<author>
<name>Florent Angly</name>
<email>[email protected]</email>
</author>
<category citation-format="numeric"/>
<category field="medicine"/>
<category field="science"/>
<issn>0767-0974</issn>
<eissn>1958-5381</eissn>
<summary>Style for the French journal Médecine / Sciences</summary>
<updated>2014-09-06T22:02:33+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="editor">
<names variable="editor" delimiter=", ">
<name initialize-with="" name-as-sort-order="all" sort-separator=" " delimiter=", " delimiter-precedes-last="always"/>
<label form="long" prefix=", "/>
</names>
</macro>
<macro name="author">
<names variable="author" suffix=".">
<name name-as-sort-order="all" sort-separator=" " initialize-with="" delimiter=", " delimiter-precedes-last="always"/>
<label form="short" prefix=" "/>
<et-al font-style="italic"/>
<substitute>
<names variable="editor"/>
<text variable="title"/>
</substitute>
</names>
</macro>
<macro name="title">
<text variable="title"/>
</macro>
<macro name="publisher">
<group delimiter=" : ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
</macro>
<macro name="year-date">
<choose>
<if variable="issued">
<date variable="issued">
<date-part name="year"/>
</date>
</if>
<else>
<text term="no date" form="short"/>
</else>
</choose>
</macro>
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" suffix="."/>
</else>
</choose>
</macro>
<citation collapse="citation-number">
<sort>
<key variable="citation-number" sort="ascending"/>
</sort>
<layout prefix="[" suffix="]" delimiter=",">
<text variable="citation-number"/>
</layout>
</citation>
<bibliography et-al-min="4" et-al-use-first="3" second-field-align="flush">
<layout>
<text variable="citation-number" suffix=". "/>
<text macro="author"/>
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=" " prefix=" ">
<text macro="title" suffix="." font-style="italic"/>
<text macro="edition"/>
<text macro="editor"/>
<text macro="publisher" suffix=","/>
<text macro="year-date" prefix=" " suffix=" :"/>
<text variable="number-of-pages"/>
<label variable="page" form="short"/>
</group>
</if>
<else-if type="chapter paper-conference" match="any">
<text macro="title" prefix=" " suffix="."/>
<group prefix=" " delimiter=". " suffix=".">
<group>
<text term="in" text-case="capitalize-first" suffix=" :"/>
<text macro="editor" prefix=" "/>
</group>
<text variable="container-title" font-style="italic"/>
<text variable="collection-title"/>
</group>
<text macro="publisher" prefix=" " suffix=","/>
<text macro="year-date" prefix=" " suffix=" :"/>
<text variable="page" prefix=" " suffix="."/>
</else-if>
<else-if type="thesis">
<group delimiter=" " prefix=" ">
<text macro="title"/>
<text variable="genre" prefix="[" suffix="]. "/>
<text macro="publisher" suffix="."/>
<text macro="year-date" prefix=" " suffix="."/>
</group>
</else-if>
<else>
<text macro="title" prefix=" " suffix="."/>
<text variable="container-title" form="short" font-style="italic" prefix=" "/>
<text macro="year-date" prefix=" " suffix=" ;"/>
<text variable="volume" prefix=" " suffix=" "/>
<text variable="page" prefix=": "/>
<text value="."/>
</else>
</choose>
</layout>
</bibliography>
</style>
1 change: 1 addition & 0 deletions inst/report_DESeq2.rmd
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Expand Up @@ -8,6 +8,7 @@ output:
toc_float: TRUE
number_sections: TRUE
bibliography: bibliography.bib
csl: medecine-sciences.csl
---

The SARTools R package which generated this report has been developped at PF2 - Institut Pasteur by M.-A. Dillies and H. Varet ([email protected]). Thanks to cite H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, _SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data_, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022 when using this tool for any analysis published.
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1 change: 1 addition & 0 deletions inst/report_edgeR.rmd
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Expand Up @@ -8,6 +8,7 @@ output:
toc_float: TRUE
number_sections: TRUE
bibliography: bibliography.bib
csl: medecine-sciences.csl
---

The SARTools R package which generated this report has been developped at PF2 - Institut Pasteur by M.-A. Dillies and H. Varet ([email protected]). Thanks to cite H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, _SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data_, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022 when using this tool for any analysis published.
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