# HG changeset patch
# User kpbioteam
# Date 1559931289 14400
# Node ID bb6c8d38fad149356faabb1a724aa466fceeaaf0
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
diff -r 000000000000 -r bb6c8d38fad1 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jun 07 14:14:49 2019 -0400
@@ -0,0 +1,18 @@
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+ @MINFI_VERSION@
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+ r-base
+ bioconductor-minfi
+ bioconductor-illuminahumanmethylation450kmanifest
+ bioconductor-rtracklayer
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+ 1.28.0
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+ 10.1093/bioinformatics/btu049
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diff -r 000000000000 -r bb6c8d38fad1 minfi_dmp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_dmp.xml Fri Jun 07 14:14:49 2019 -0400
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+ to find differentially methylated positions
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+ macros.xml
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diff -r 000000000000 -r bb6c8d38fad1 minfi_dmr.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_dmr.xml Fri Jun 07 14:14:49 2019 -0400
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+ to find differentially methylated regions
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+ macros.xml
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diff -r 000000000000 -r bb6c8d38fad1 minfi_dropsnp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_dropsnp.xml Fri Jun 07 14:14:49 2019 -0400
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+ drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension
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+ macros.xml
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+bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19
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diff -r 000000000000 -r bb6c8d38fad1 minfi_getbeta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getbeta.xml Fri Jun 07 14:14:49 2019 -0400
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+ obtain Beta value matrix
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+ macros.xml
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diff -r 000000000000 -r bb6c8d38fad1 minfi_getcn.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getcn.xml Fri Jun 07 14:14:49 2019 -0400
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+ get the coordinating node associated with this D1Client object
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+ macros.xml
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diff -r 000000000000 -r bb6c8d38fad1 minfi_getm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getm.xml Fri Jun 07 14:14:49 2019 -0400
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+ returns the Fisher information corresponding to a model and a design
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+ macros.xml
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diff -r 000000000000 -r bb6c8d38fad1 minfi_getsnp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getsnp.xml Fri Jun 07 14:14:49 2019 -0400
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+ retrieve the chromosome and the position of each SNP
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+ macros.xml
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+ bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19
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diff -r 000000000000 -r bb6c8d38fad1 minfi_maptogenome.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_maptogenome.xml Fri Jun 07 14:14:49 2019 -0400
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+ mapping Ilumina methylation array data to the genome
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+ macros.xml
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+ bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19
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diff -r 000000000000 -r bb6c8d38fad1 minfi_mset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_mset.xml Fri Jun 07 14:14:49 2019 -0400
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+ Create objects contains CpGs signals
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+ macros.xml
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diff -r 000000000000 -r bb6c8d38fad1 minfi_ppfun.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppfun.xml Fri Jun 07 14:14:49 2019 -0400
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+ implements the functional normalization algorithm
+ macros.xml
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+ bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19
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diff -r 000000000000 -r bb6c8d38fad1 minfi_ppquantile.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppquantile.xml Fri Jun 07 14:14:49 2019 -0400
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+ implements stratified quantile normalization preprocessing
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+ macros.xml
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+ bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19
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diff -r 000000000000 -r bb6c8d38fad1 minfi_qc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_qc.xml Fri Jun 07 14:14:49 2019 -0400
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+ provides a simple quality control matrix and plot
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+ macros.xml
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diff -r 000000000000 -r bb6c8d38fad1 minfi_read450k.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_read450k.xml Fri Jun 07 14:14:49 2019 -0400
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+ load .IDAT files
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+ bioconductor-minfi
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+ 10.18129/B9.bioc.illuminaio
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diff -r 000000000000 -r bb6c8d38fad1 minfi_rset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_rset.xml Fri Jun 07 14:14:49 2019 -0400
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+ store Beta values and/or M values
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+ macros.xml
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