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added:
GEO/.Rhistory GEO/._.DS_Store GEO/getGEO.R GEO/getGEO.xml GEO/test-data/._.DS_Store GEO/test-data/._input.csv GEO/test-data/MetaTable.csv GEO/test-data/input.csv GEO/tool_dependencies.xml |
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removed:
geo_data-05050b50d4f8/GEO/.Rhistory geo_data-05050b50d4f8/GEO/._.DS_Store geo_data-05050b50d4f8/GEO/getGEO.R geo_data-05050b50d4f8/GEO/getGEO.xml geo_data-05050b50d4f8/GEO/test-data/._.DS_Store geo_data-05050b50d4f8/GEO/test-data/._input.csv geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv geo_data-05050b50d4f8/GEO/test-data/gmTable.csv geo_data-05050b50d4f8/GEO/test-data/input.csv geo_data-05050b50d4f8/GEO/tool_dependencies.xml |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEO/.Rhistory Mon Feb 20 08:11:50 2017 -0500 |
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| @@ -0,0 +1,7 @@ +??options +options(warn = -1) ++options("download.file.method"="wget") +options("download.file.method"="wget") +options(warn = -1,"download.file.method"="wget") +??getPlatform +??getPlatform |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/._.DS_Store |
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| Binary file GEO/._.DS_Store has changed |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/getGEO.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEO/getGEO.R Mon Feb 20 08:11:50 2017 -0500 |
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| @@ -0,0 +1,54 @@ +require("BiocGenerics", quietly = TRUE) +require("data.table", quietly = TRUE) +require("GEOquery", quietly = TRUE) +require("rtracklayer", quietly = TRUE) +require("FDb.InfiniumMethylation.hg19", quietly = TRUE) + +options("download.file.method.GEOquery"="wget") +options(warn = -1) + +args <- commandArgs(trailingOnly = TRUE) +GSMTable = args[1] +protocol = args[2] +platform = args[3] +Data_Table = args[4] + +TAB = fread(GSMTable) + +if (is.null(TAB)) { + stop("Must specify input files") +} else { + GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) + IlmnIDTable <- Table(GEODataTable) + MetaData <- data.frame(Meta(GEODataTable)) + + + write.csv(MetaData, protocol, row.names = FALSE, sep = "\t") +} + +hm450.hg19 <- getPlatform() + +IlmnInfo <- + data.table( + IlmnID = names(hm450.hg19), + CHR = as.data.frame(hm450.hg19@seqnames)$value, + BP = as.numeric(hm450.hg19@elementMetadata$probeStart) + ) + + +write.csv(IlmnInfo, platform, row.names = FALSE, sep = "\t") + + +if (length(TAB$ID) > 1) { + mysamples <- + do.call("data.table", lapply(TAB$ID[-1], function(x) + Table(getGEO(x, getGPL = FALSE))[, -1])) + + gmSet <- data.table(IlmnIDTable[, -1], mysamples) + +} else { + gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE)) +} + + +write.csv(gmSet, Data_Table, row.names = FALSE, sep = "\t") |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/getGEO.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEO/getGEO.xml Mon Feb 20 08:11:50 2017 -0500 |
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| @@ -0,0 +1,39 @@ +<tool id="GEO" name="getGEO" version="1.16.2"> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + </requirements> +<stdio> + <exit_code range="1:" /> + </stdio> + <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$protocol" "$platform" "$Data_Table"</command> + <inputs> + <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="csv" name="protocol" label="protocol.csv"/> + <data format="csv" name="platform" label="platform.csv"/> + <data format="csv" name="Data_Table" label="Data_Table.csv"/> + </outputs> + <tests> + <test> + <param name="test"> + <element name="test-data"> + <collection type="data"> + <element name="GSMTable" value="test-data/input.csv" /> + </collection> + </element> + </param> + <output format="csv" name="protocol" label="test-data/protocol.csv"/> + <output format="csv" name="platform" label="test-data/platform.csv"/> + <output format="csv" name="Data_Table" label="test-data/Data_Table.csv"/> + </test> + </tests> + <help> +**Description** +</help> +<citations> +GEO +</citations> +</tool> |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/test-data/._.DS_Store |
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| Binary file GEO/test-data/._.DS_Store has changed |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/test-data/._input.csv |
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| Binary file GEO/test-data/._input.csv has changed |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/test-data/MetaTable.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEO/test-data/MetaTable.csv Mon Feb 20 08:11:50 2017 -0500 |
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| @@ -0,0 +1,2 @@ +"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" +"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/test-data/input.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEO/test-data/input.csv Mon Feb 20 08:11:50 2017 -0500 |
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| @@ -0,0 +1,4 @@ +ID,Phenotype +GSM1247787,melanoma +GSM1247784,melanoma +GSM1247733,healthy |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b GEO/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEO/tool_dependencies.xml Mon Feb 20 08:11:50 2017 -0500 |
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| b'@@ -0,0 +1,273 @@\n+<?xml version="1.0"?>\n+<tool_dependency>\n+ <install version="1.0">\n+ <actions>\n+ <action type="setup_r_environment">\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="R" version="3.2.1"/>\n+ </repository>\n+ <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n+ https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n+ </package>\n+ <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n+ https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n+ </package>\n+ <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n+ https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n+ </package>\n+ <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n+ 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sha256sum="51a74de64296d7cbed04a015a9f9725de95adb5e04301d1cd58190d7365fb104">\n+ https://bioarchive.galaxyproject.org/biomaRt_2.31.3.tar.gz\n+ </package>\n+ <package sha256sum="801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f">\n+ https://depot.galaxyproject.org/software/gtable/gtable_0.2.0.tar.gz\n+ </package>\n+ <package sha256sum="ed8a8bd0591223f742be80fd1cd8c4a9618d0f04011ec95c272b61ea45193104">\n+ https://depot.galaxyproject.org/software/tibble/tibble_1.2.tar.gz\n+ </package>\n+ <package sha256sum="13738f55b2044184fe91f53d17516a445dfb508227527921218cda6f01f98dcb">\n+ https://depot.galaxyproject.org/software/lazyeval/lazyeval_0.2.0.tar.gz\n+ </package>\n+ <package sha256sum="8097ec0e4868f6bf746f821cff7842f696e874bb3a84f1b2aa977ecd961c3e4e">\n+ https://depot.galaxyproject.org/software/gdata/gdata_2.17.0.tar.gz\n+ </package>\n+ <package sha256sum="d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4">\n+ https://depot.galaxyproject.org/software/caTools/caTools_1.17.1.tar.gz\n+ </package>\n+ <package sha256sum="1363645a9a128f6'..b' <package sha256sum="d89db98ea1025e38d59daeff965dd8174bbb94a961cb966a83760ac1a87a36b8">\n+ https://depot.galaxyproject.org/software/reshape/reshape_0.8.6.tar.gz\n+ </package>\n+ <package sha256sum="d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349">\n+ https://depot.galaxyproject.org/software/quadprog/quadprog_1.5-5.tar.gz\n+ </package>\n+ <package sha256sum="cd26dbd60b2e2060541c4bb579ec1e0f6c262501431460b096b5fef323204432">\n+ https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz\n+ </package>\n+ <package sha256sum="bee70645c7cc88250761092762a9d293b4644f311047baecf49fde766d3059bc">\n+ https://bioarchive.galaxyproject.org/Biobase_2.35.0.tar.gz\n+ </package>\n+ <package sha256sum="c6133611cc991dfc17410d06a9ddcc6dcff0153bceffdf7d5a9b7dc42f31afa6">\n+ https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.4.0.tar.gz\n+ 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https://depot.galaxyproject.org/software/fastmatch/fastmatch_1.0-4.tar.gz\n+ </package>\n+ <package sha256sum="5183e8dd7943df11c0f44460566adf06c03d5320f142699298f516d423b06ce1">\n+ https://depot.galaxyproject.org/software/irlba/irlba_2.1.2.tar.gz\n+ </package>\n+ <package sha256sum="19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f">\n+ https://depot.galaxyproject.org/software/pkgmaker/pkgmaker_0.22.tar.gz\n+ </package>\n+ <package sha256sum="58a5c43b8012ca5e509fa29a8daf6f24f097b8eb021a723f6a9c33db1dd3f430">\n+ https://depot.galaxyproject.org/software/registry/registry_0.3.tar.gz\n+ </package>\n+ <package sha256sum="27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9">\n+ https://depot.galaxyproject.org/software/rngtools/rngtools_1.2.4.tar.gz\n+ </package>\n+ <package sha256sum="605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f">\n+ https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz\n+ </package>\n+ </action>\n+ </actions>\n+ </install>\n+ </tool_dependency>\n' |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/.Rhistory --- a/geo_data-05050b50d4f8/GEO/.Rhistory Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -??options -options(warn = -1) -+options("download.file.method"="wget") -options("download.file.method"="wget") -options(warn = -1,"download.file.method"="wget") -??getPlatform -??getPlatform |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/._.DS_Store |
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| Binary file geo_data-05050b50d4f8/GEO/._.DS_Store has changed |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/getGEO.R --- a/geo_data-05050b50d4f8/GEO/getGEO.R Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,54 +0,0 @@ -require("BiocGenerics", quietly = TRUE) -require("data.table", quietly = TRUE) -require("GEOquery", quietly = TRUE) -require("rtracklayer", quietly = TRUE) -require("FDb.InfiniumMethylation.hg19", quietly = TRUE) - -options("download.file.method.GEOquery"="wget") -options(warn = -1) - -args <- commandArgs(trailingOnly = TRUE) -GSMTable = args[1] -MetaTable = args[2] -IlmnTable = args[3] -gmTable = args[4] - -TAB = fread(GSMTable) - -if (is.null(TAB)) { - stop("Must specify input files") -} else { - GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) - IlmnIDTable <- Table(GEODataTable) - MetaData <- data.frame(Meta(GEODataTable)) - - - write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t") -} - -hm450.hg19 <- getPlatform() - -IlmnInfo <- - data.table( - IlmnID = names(hm450.hg19), - CHR = as.data.frame(hm450.hg19@seqnames)$value, - BP = as.numeric(hm450.hg19@elementMetadata$probeStart) - ) - - -write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t") - - -if (length(TAB$ID) > 1) { - mysamples <- - do.call("data.table", lapply(TAB$ID[-1], function(x) - Table(getGEO(x, getGPL = FALSE))[, -1])) - - gmSet <- data.table(IlmnIDTable[, -1], mysamples) - -} else { - gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE)) -} - - -write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t") |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/getGEO.xml --- a/geo_data-05050b50d4f8/GEO/getGEO.xml Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,39 +0,0 @@ -<tool id="GEO" name="getGEO" version="1.16.2"> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> -<stdio> - <exit_code range="1:" /> - </stdio> - <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command> - <inputs> - <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable"> - <validator type="empty_field" message="This field is required."/> - </param> - </inputs> - <outputs> - <data format="csv" name="MetaTable" label="MetaData.csv"/> - <data format="csv" name="IlmnTable" label="IlmnData.csv"/> - <data format="csv" name="gmTable" label="gmSet.csv"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSMTable" value="test-data/input.csv" /> - </collection> - </element> - </param> - <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/> - <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/> - <output format="csv" name="gmTable" label="test-data/gmTable.csv"/> - </test> - </tests> - <help> -**Description** -</help> -<citations> -GEO -</citations> -</tool> |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/test-data/._.DS_Store |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/test-data/._input.csv |
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| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv --- a/geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,485578 +0,0 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|
| b |
| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv --- a/geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" -"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
| b |
| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/test-data/gmTable.csv --- a/geo_data-05050b50d4f8/GEO/test-data/gmTable.csv Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/test-data/input.csv --- a/geo_data-05050b50d4f8/GEO/test-data/input.csv Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -ID,Phenotype -GSM1247787,melanoma -GSM1247784,melanoma -GSM1247733,healthy |
| b |
| diff -r 6bd7af1bcb43 -r 5231cb49c63b geo_data-05050b50d4f8/GEO/tool_dependencies.xml --- a/geo_data-05050b50d4f8/GEO/tool_dependencies.xml Fri Feb 10 08:38:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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