Man pages for microbiome/HITChipDB
HITChipDB

add.heatmapadd.heatmap
calculate.hclustcalculate.hclust
choose.projectsDescription: Select projects to analyze
choose.sampleschoose.samples
detect.chipDescription: Detect the chip type (H/M/PITChip) from database...
estimate.min.thresholdDescription: determine threshold for bg correction
expandConditionExpands a list of "field", "value" pair lists into an SQL...
expandElementExpands one element (one "field", "value" pair list) from a...
FetchDataFetch data from the database
fetch.projectsfetch.projects
fetch.sample.infofetch.sample.info
fetch.samplesFetch samples from a phyloarray database
get.doligo2Description: Calculate d.oligo2
get_hitchip_taxonomyHITChip Taxonomy Table
get.phylogeny.infoget.phylogeny.info
get.probedataDescription: Get probedata
get.sampleidDescription: Pick sampleIDs from d.oligo column names
hitchip2physeqHITChip to phyloseq
HITChipDB-packageR package for HITChipDB studies
htree.plothtree.plot
import_hitchipImport HITChip data
list.color.scalesList color scales
list.mysql.projectslist.mysql.projects
mysql.formatDescription: Format string vector to mysql query format
n.phylotypes.per.oligoDescription: Check number of matching phylotypes for each...
oligo.bg.correctionDescription: Calculate species summaries and possibly update...
phyloarrayConnectionTests whether the database connection is a phyloarray...
phylotype.rm.listDefault list of removed phylotypes and oligos
PlotPhylochipHeatmapPlotPhylochipHeatmap
populate.radiobuttonsDescription: populate radiobuttons
preprocess.chipdataDescription: Profiling preprocessing script
prune16SDescription: filter 16S data
read_hitchipRead HITChip
ReadParametersDefine parameters in select box
ReadPhylogenyRead phylogeny
relative.abundanceRelative abundance
retrieve.probesetsretrieve.probesets
run.profiling.scriptRun profiling script
ScaleProfileDescription: Between-arrays normalization
scaling.minmaxDescription: Minmax scaling.
summarize.rawdataDescription: Compress normalized raw data matrix into final...
summarize.rpaDescription: Probeset summarization with RPA
summarize.sumProbeset summarization with SUM
sync.rm.phylotypesDescription: List oligos associated with removed phylotypes...
threshold.dataDescription: determine detection threshold for the data
WriteChipDataDescription: Writed data into the output directory
WriteLogDescription: Write log file
WriteMatrixDescription: Write matrix in tab file
microbiome/HITChipDB documentation built on July 18, 2017, 3:43 p.m.