systemPipeR: NGS workflow and report generation environment


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Documentation for package ‘systemPipeR’ version 1.0.12

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A C F G I L M N O P Q R S T V W misc

-- A --

alignStats Alignment statistics
as.list-method Class '"INTERSECTset"'
as.list-method Class '"VENNset"'

-- C --

catDB-class Class '"catDB"'
catlist catDB accessor methods
catlist-method Class '"catDB"'
catlist-methods catDB accessor methods
catmap catDB accessor methods
catmap-method Class '"catDB"'
catmap-methods catDB accessor methods
clusterRun Submit command-line tools to cluster
coerce-method Class '"INTERSECTset"'
coerce-method Class '"SYSargs"'
coerce-method Class '"VENNset"'
coerce-method Class '"catDB"'
complexitylevels Set Intersect and Venn Diagram Functions
complexitylevels-method Class '"INTERSECTset"'
complexitylevels-method Class '"VENNset"'
complexitylevels-methods Set Intersect and Venn Diagram Functions
cores SYSargs accessor methods
cores-method Class '"SYSargs"'
cores-methods SYSargs accessor methods

-- F --

filterDEGs Filter and plot DEG results

-- G --

getQsubargs Arguments for qsub
goBarplot GO term enrichment analysis for large numbers of gene sets
GOCluster_Report GO term enrichment analysis for large numbers of gene sets
GOHyperGAll GO term enrichment analysis for large numbers of gene sets
GOHyperGAll_Simplify GO term enrichment analysis for large numbers of gene sets
GOHyperGAll_Subset GO term enrichment analysis for large numbers of gene sets

-- I --

idconv catDB accessor methods
idconv-method Class '"catDB"'
idconv-methods catDB accessor methods
infile1 SYSargs accessor methods
infile1-method Class '"SYSargs"'
infile1-methods SYSargs accessor methods
infile2 SYSargs accessor methods
infile2-method Class '"SYSargs"'
infile2-methods SYSargs accessor methods
intersectlist Set Intersect and Venn Diagram Functions
intersectlist-method Class '"INTERSECTset"'
intersectlist-methods Set Intersect and Venn Diagram Functions
intersectmatrix Set Intersect and Venn Diagram Functions
intersectmatrix-method Class '"INTERSECTset"'
intersectmatrix-method Class '"VENNset"'
intersectmatrix-methods Set Intersect and Venn Diagram Functions
INTERSECTset-class Class '"INTERSECTset"'

-- L --

length-method Class '"INTERSECTset"'
length-method Class '"SYSargs"'
length-method Class '"VENNset"'

-- M --

makeCATdb GO term enrichment analysis for large numbers of gene sets
modulelist Interface to module system
moduleload Interface to module system
modules SYSargs accessor methods
modules-method Class '"SYSargs"'
modules-methods SYSargs accessor methods

-- N --

names-method Class '"INTERSECTset"'
names-method Class '"SYSargs"'
names-method Class '"VENNset"'
names-method Class '"catDB"'

-- O --

olBarplot Bar plot for intersect sets
other SYSargs accessor methods
other-method Class '"SYSargs"'
other-methods SYSargs accessor methods
outfile1 SYSargs accessor methods
outfile1-method Class '"SYSargs"'
outfile1-methods SYSargs accessor methods
outpaths SYSargs accessor methods
outpaths-method Class '"SYSargs"'
outpaths-methods SYSargs accessor methods
overLapper Set Intersect and Venn Diagram Functions

-- P --

preprocessReads Run custom read preprocessing functions

-- Q --

qsubRun Submit command-line tools to cluster

-- R --

readComp Import sample comparisons from targets file
reference SYSargs accessor methods
reference-method Class '"SYSargs"'
reference-methods SYSargs accessor methods
results SYSargs accessor methods
results-method Class '"SYSargs"'
results-methods SYSargs accessor methods
returnRPKM RPKM Normalization
runCommandline Execute SYSargs
run_DESeq2 Runs DESeq2
run_edgeR Runs edgeR

-- S --

SampleName SYSargs accessor methods
SampleName-method Class '"SYSargs"'
SampleName-methods SYSargs accessor methods
seeFastq Quality reports for FASTQ files
seeFastqPlot Quality reports for FASTQ files
setlist Set Intersect and Venn Diagram Functions
setlist-method Class '"INTERSECTset"'
setlist-method Class '"VENNset"'
setlist-methods Set Intersect and Venn Diagram Functions
show-method Class '"INTERSECTset"'
show-method Class '"SYSargs"'
show-method Class '"VENNset"'
show-method Class '"catDB"'
software SYSargs accessor methods
software-method Class '"SYSargs"'
software-methods SYSargs accessor methods
symLink2bam Symbolic links for IGV
sysargs SYSargs accessor methods
SYSargs-class Class '"SYSargs"'
sysargs-method Class '"SYSargs"'
sysargs-methods SYSargs accessor methods
systemArgs Constructs SYSargs object from param and targets files

-- T --

targetsheader SYSargs accessor methods
targetsheader-method Class '"SYSargs"'
targetsheader-methods SYSargs accessor methods
targetsin SYSargs accessor methods
targetsin-method Class '"SYSargs"'
targetsin-methods SYSargs accessor methods
targetsout SYSargs accessor methods
targetsout-method Class '"SYSargs"'
targetsout-methods SYSargs accessor methods

-- V --

vennlist Set Intersect and Venn Diagram Functions
vennlist-method Class '"VENNset"'
vennlist-methods Set Intersect and Venn Diagram Functions
vennPlot Plot 2-5 way Venn diagrams
VENNset-class Class '"VENNset"'

-- W --

writeTargetsout Write updated targets out to file

-- misc --

[-method Class '"SYSargs"'