Mercurial > repos > mingchen0919 > rmarkdown_deseq2

annotate DESeq.xml @ 9:924d122d0027 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
change data format
author mingchen0919
date Thu, 16 Nov 2017 10:16:29 -0500
parents 5f7665898fd9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
466053167103 update deseq2
mingchen0919
parents: 6
diff changeset
1 <tool id="DESeq" name="DESeq2: DESeq" version="2.0.0">
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
2 <requirements>
5
fd3514267506 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
mingchen0919
parents: 4
diff changeset
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
4 <requirement type="package" version="1.20.0">r-getopt</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
6 <requirement type="package" version="1.8.4">r-plyr</requirement>
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
7 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
8 <requirement type="package" version="1.1.0">r-stringr</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
9 <requirement type="package" version="0.4.0">r-highcharter</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
10 <requirement type="package" version="0.2">r-dt</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
11 <requirement type="package" version="1.4.2">r-reshape2</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
12 <requirement type="package" version="4.5.6">r-plotly</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
13 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
14 <requirement type="package" version="0.3.5">r-htmltools</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
15 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
16 </requirements>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
17 <description>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
18 An R Markdown tool to perform DESeq analysis.
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
19 </description>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
20 <stdio>
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
21 <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
22 <regex match="XXX"
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
23 source="stderr"
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
24 level="warning"
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
25 description="Check the warnings_and_errors.txt file for more details."/>
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
26 </stdio>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
27 <command>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
28 <![CDATA[
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
29
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
30 Rscript '${__tool_directory__}/DESeq_render.R'
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
31
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
32
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
33 ## 1. input data
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
34 -e $echo
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
35 ##----- code chunk to get file paths and raw file names for a multiple inputs data field ----
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
36 #set $sep = ''
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
37 #set $count_file_paths = ''
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
38 #set $count_file_names = ''
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
39 #for $count_file in $count_files:
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
40 #set $count_file_paths += $sep + str($count_file)
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
41 #set $count_file_names += $sep + str($count_file.name)
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
42 #set $sep = ','
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
43 #end for
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
44 ##----------------- end for getting file names and file paths ------------------------------
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
45 -P '$count_file_paths'
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
46 -N '$count_file_names'
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
47 -S $sample_table
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
48 -p '$design_formula'
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
49
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
50 ## 2. output report and report site directory
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
51 -r $report
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
52 -d $report.files_path
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
53 -s $sink_message
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
54 -w $deseq_workspace
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
55
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
56 ## 3. Rmd templates from the tool directory
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
57 -t '${__tool_directory__}/DESeq.Rmd'
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
58
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
59
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
60
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
61 ]]>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
62 </command>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
63 <inputs>
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
64 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
65 label="Display analysis code in report?"/>
9
924d122d0027 change data format
mingchen0919
parents: 8
diff changeset
66 <param type="data" name="count_files" format="txt" multiple="true" label="Count files from htseq-count"/>
924d122d0027 change data format
mingchen0919
parents: 8
diff changeset
67 <param type="data" name="sample_table" format="txt" multiple="false" label="sample table file"
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
68 help="The sample table file contains a table. The first column is the sample name, the second column is
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
69 the count file name and the rest of columns are treatment columns. The file names in this table have
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
70 to be in the same order as the count files uploaded in the previous step. "/>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
71 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
72 help="The simplest design formula for differential expression would be ~ condition, where condition
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
73 is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
74 <sanitizer>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
75 <valid initial="default">
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
76 <add preset="string.printable"/>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
77 <add value="~"/>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
78 </valid>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
79 </sanitizer>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
80 </param>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
81 </inputs>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
82 <outputs>
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
83 <data name="report" format="html" label="DESeq Analysis on ${on_string}"/>
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
84 <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
85 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis on ${on_string}"/>
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
86 </outputs>
3
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
87 <citations>
8
5f7665898fd9 fix citation error
mingchen0919
parents: 7
diff changeset
88 <citation type="bibtex">
3
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
89 @article{love2014moderated,
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
90 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
91 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
92 journal={Genome biology},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
93 volume={15},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
94 number={12},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
95 pages={550},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
96 year={2014},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
97 publisher={BioMed Central}
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
98 }
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
99 </citation>
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
100 <citation type="bibtex">
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
101 @article{allaire2016rmarkdown,
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
102 title={rmarkdown: Dynamic Documents for R, 2016},
6
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
103 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
2f8ddef8d545 update deseq2
mingchen0919
parents: 5
diff changeset
104 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
3
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
105 journal={R package version 0.9},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
106 volume={6},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
107 year={2016}
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
108 }
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
109 </citation>
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
110 <citation type="bibtex">
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
111 @book{xie2015dynamic,
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
112 title={Dynamic Documents with R and knitr},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
113 author={Xie, Yihui},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
114 volume={29},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
115 year={2015},
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
116 publisher={CRC Press}
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
117 }
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
118 </citation>
15a5fb1a2ac8 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents: 0
diff changeset
119 </citations>
0
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
diff changeset
120 </tool>