# HG changeset patch
# User malex
# Date 1624047683 0
# Node ID 864fc643043265418c7e27c3b4154643dd4eb747
Initial upload of 21.6.10 release.
diff -r 000000000000 -r 864fc6430432 gait_gm/add_kegg_anno_info.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/add_kegg_anno_info.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,219 @@
+
+
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+ macros.xml
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+ (dataSets['whichDataSet'] == 'geneDataset') or (dataSets['whichDataSet'] == 'geneDataset,metDataset')
+
+
+ (dataSets['whichDataSet'] == 'metDataset') or (dataSets['whichDataSet'] == 'geneDataset,metDataset')
+
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+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+
+ @article{garcia2010paintomics,
+ title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+ author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={Bioinformatics},
+ volume={27},
+ number={1},
+ pages={137--139},
+ year={2010},
+ publisher={Oxford University Press}
+ }
+ @article{wu2014mygene,
+ title={MyGene. info: gene annotation query as a service},
+ author={Wu, Chunlei and Mark, Adam and Su, Andrew I},
+ journal={bioRxiv},
+ pages={009332},
+ year={2014},
+ publisher={Cold Spring Harbor Laboratory}
+ }
+
+
diff -r 000000000000 -r 864fc6430432 gait_gm/add_kegg_pathway_info.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/add_kegg_pathway_info.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,239 @@
+
+ using KEGGIDs
+
+ macros.xml
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+ (dataSets['whichDataSet'] == 'geneDataset') or (dataSets['whichDataSet'] == 'both')
+
+
+ (dataSets['whichDataSet'] == 'metDataset') or (dataSets['whichDataSet'] == 'both')
+
+
+
+ (dataSets['whichDataSet'] == 'geneDataset') or (dataSets['whichDataSet'] == 'both')
+
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+ (dataSets['whichDataSet'] == 'metDataset') or (dataSets['whichDataSet'] == 'both')
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+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+ @article{garcia2010paintomics,
+ title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+ author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={Bioinformatics},
+ volume={27},
+ number={1},
+ pages={137--139},
+ year={2010},
+ publisher={Oxford University Press}
+ }
+
+
diff -r 000000000000 -r 864fc6430432 gait_gm/add_pval_flags.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/add_pval_flags.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,140 @@
+
+ using custom thresholds
+
+ macros.xml
+
+
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+
+
+
+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+ @article{garcia2010paintomics,
+ title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+ author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={Bioinformatics},
+ volume={27},
+ number={1},
+ pages={137--139},
+ year={2010},
+ publisher={Oxford University Press}
+ }
+
+
diff -r 000000000000 -r 864fc6430432 gait_gm/all_by_all_correlation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/all_by_all_correlation.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,216 @@
+
+
+
+ macros.xml
+
+
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+
+ @article{dejean2013mixomics,
+ title={mixOmics: Omics data integration project},
+ author={Dejean, Sebastien and Gonzalez, Ignacio and L{\^e} Cao, Kim-Anh and Monget, Pierre and Coquery, J and Yao, F and Liquet, B and Rohart, F},
+ journal={R package},
+ year={2013}
+ }
+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+
+ @article{garcia2010paintomics,
+ title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+ author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={Bioinformatics},
+ volume={27},
+ number={1},
+ pages={137--139},
+ year={2010},
+ publisher={Oxford University Press}
+ }
+
+
diff -r 000000000000 -r 864fc6430432 gait_gm/ensembl2symbol.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/ensembl2symbol.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,126 @@
+
+
+
+ macros.xml
+
+
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+
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+
+
+
+ @article{wu2014mygene,
+ title={MyGene. info: gene annotation query as a service},
+ author={Wu, Chunlei and Mark, Adam and Su, Andrew I},
+ journal={bioRxiv},
+ pages={009332},
+ year={2014},
+ publisher={Cold Spring Harbor Laboratory}
+ }
+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+
+ @article{garcia2010paintomics,
+ title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+ author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={Bioinformatics},
+ volume={27},
+ number={1},
+ pages={137--139},
+ year={2010},
+ publisher={Oxford University Press}
+ }
+
+
diff -r 000000000000 -r 864fc6430432 gait_gm/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/macros.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,145 @@
+
+
+ 21.6.10
+
+
+ gait-gm
+
+
+
+
+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+
+
+
+
+ **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
+
+ **WARNINGS:**
+
+ (1) SampleIDs in the wide data that have no matching name in the design file, as well as sampleIDs in the design file that have no match in data will be included in the analysis.
+ (2) This script automatically removes spaces and special characters from strings.
+ (3) If a compound/feature name starts with a number it will prepend an '_'.
+ (4) Input names are case sensitive and must match exactly (e.g use 'Feature' not 'feature').
+
+
+ **Wide Formatted Dataset**
+
+ A wide formatted dataset that contains measurements for each sample:
+
+ +---------+---------+---------+---------+-----+
+ | Feature | sample1 | sample2 | sample3 | ... |
+ +=========+=========+=========+=========+=====+
+ | one | 10 | 20 | 10 | ... |
+ +---------+---------+---------+---------+-----+
+ | two | 5 | 22 | 30 | ... |
+ +---------+---------+---------+---------+-----+
+ | three | 30 | 27 | 2 | ... |
+ +---------+---------+---------+---------+-----+
+ | four | 32 | 17 | 8 | ... |
+ +---------+---------+---------+---------+-----+
+ | ... | ... | ... | ... | ... |
+ +---------+---------+---------+---------+-----+
+
+ **NOTE:** The 'Feature' column defines the rows within a wide formatted dataset.
+
+
+ **Design File**
+
+ A Design file relating samples to various groups/treatment:
+
+ +----------+--------+
+ | sampleID | group |
+ +==========+========+
+ | sample1 | g1 |
+ +----------+--------+
+ | sample2 | g1 |
+ +----------+--------+
+ | sample3 | g1 |
+ +----------+--------+
+ | sample4 | g2 |
+ +----------+--------+
+ | sample5 | g2 |
+ +----------+--------+
+ | sample6 | g2 |
+ +----------+--------+
+ | ... | ... |
+ +----------+--------+
+
+ **NOTE:** You must have a column named **sampleID** and the values in this column must match the column names in the wide dataset.
+
+
+ **Flag File:**
+
+ A wide formated dataset that contains flags for each sample or feature:
+
+ +----------+---------+---------+---------+-----+
+ | Feature | flag_A | flag_B | flag_C | ... |
+ +==========+=========+=========+=========+=====+
+ | one | 0 | 0 | 0 | ... |
+ +----------+---------+---------+---------+-----+
+ | two | 0 | 1 | 1 | ... |
+ +----------+---------+---------+---------+-----+
+ | three | 0 | 1 | 0 | ... |
+ +----------+---------+---------+---------+-----+
+ | four | 1 | 0 | 0 | ... |
+ +----------+---------+---------+---------+-----+
+ | ... | ... | ... | ... | ... |
+ +----------+---------+---------+---------+-----+
+
+
+
+ **M/Z RT File:**
+
+ A wide formated dataset that contains M/Z and RT measurements for each sample:
+
+ +----------+--------+----------------+
+ | sampleID | M/Z | Retention Time |
+ +==========+========+================+
+ | sample1 | 0.1556 | 0.253618769 |
+ +----------+--------+----------------+
+ | sample2 | 0.1675 | 0.327658519 |
+ +----------+--------+----------------+
+ | sample3 | 0.1341 | 0.156587769 |
+ +----------+--------+----------------+
+ | sample4 | 0.2341 | 0.153658165 |
+ +----------+--------+----------------+
+ | sample5 | 0.4557 | 0.315765787 |
+ +----------+--------+----------------+
+ | sample6 | 0.1879 | 0.253655765 |
+ +----------+--------+----------------+
+ | ... | ... | ... |
+ +----------+--------+----------------+
+
+
+
+ **Group/Treatment [Optional]**
+
+ - Name of the column in your Design File that contains group classifications.
+
+
+ **Group/Treatment**
+
+ - Name of the column in your Design File that contains group classifications.
+
+
+ **Unique Feature ID**
+
+ - Name of the column in your Wide Dataset that has unique Feature IDs.
+
+
+ **Run Order ID**
+
+ - The column name in your Design file that contains the order samples were run.
+
+
+ **Run Order ID [Optional]**
+
+ - The column name in your Design file that contains the order samples were run.
+
+
diff -r 000000000000 -r 864fc6430432 gait_gm/sPLS.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/sPLS.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,464 @@
+
+
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+ macros.xml
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+ (metsOption['allMets'] == 'mmc') or (metsOption['allMets'] == 'both')
+
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+ (metsOption['allMets'] == 'mmc') or (metsOption['allMets'] == 'both')
+
+
+ (metsOption['genesOption']['allGenes'] == 'pana')
+
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+
+ @article{ponzoni2014pathway,
+ title={Pathway network inference from gene expression data},
+ author={Ponzoni, Ignacio and Nueda, Mar{\'\i}a Jos{\'e} and Tarazona, Sonia and G{\"o}tz, Stefan and Montaner, David and Dussaut, Julieta Sol and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={BMC systems biology},
+ volume={8},
+ number={2},
+ pages={S7},
+ year={2014},
+ publisher={BioMed Central}
+ }
+ @article{dejean2013mixomics,
+ title={mixOmics: Omics data integration project},
+ author={Dejean, Sebastien and Gonzalez, Ignacio and L{\^e} Cao, Kim-Anh and Monget, Pierre and Coquery, J and Yao, F and Liquet, B and Rohart, F},
+ journal={R package},
+ year={2013}
+ }
+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+
+ @article{garcia2010paintomics,
+ title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+ author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={Bioinformatics},
+ volume={27},
+ number={1},
+ pages={137--139},
+ year={2010},
+ publisher={Oxford University Press}
+ }
+
+
diff -r 000000000000 -r 864fc6430432 gait_gm/split_wide_dataset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gait_gm/split_wide_dataset.xml Fri Jun 18 20:21:23 2021 +0000
@@ -0,0 +1,205 @@
+
+ from an Input wide dataset
+
+ macros.xml
+
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+
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+ @ARTICLE{Kirpich17secimtools,
+ author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+ title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+ journal = {BMC Bioinformatics},
+ year = {in press}
+ }
+ @article{garcia2010paintomics,
+ title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+ author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+ journal={Bioinformatics},
+ volume={27},
+ number={1},
+ pages={137--139},
+ year={2010},
+ publisher={Oxford University Press}
+ }
+
+