Man pages for microbiome/HITChipDB
HITChipDB
| add.heatmap | add.heatmap |
| calculate.hclust | calculate.hclust |
| choose.projects | Description: Select projects to analyze |
| choose.samples | choose.samples |
| detect.chip | Description: Detect the chip type (H/M/PITChip) from database... |
| estimate.min.threshold | Description: determine threshold for bg correction |
| expandCondition | Expands a list of "field", "value" pair lists into an SQL... |
| expandElement | Expands one element (one "field", "value" pair list) from a... |
| FetchData | Fetch data from the database |
| fetch.projects | fetch.projects |
| fetch.sample.info | fetch.sample.info |
| fetch.samples | Fetch samples from a phyloarray database |
| get.doligo2 | Description: Calculate d.oligo2 |
| get_hitchip_taxonomy | HITChip Taxonomy Table |
| get.phylogeny.info | get.phylogeny.info |
| get.probedata | Description: Get probedata |
| get.sampleid | Description: Pick sampleIDs from d.oligo column names |
| hitchip2physeq | HITChip to phyloseq |
| HITChipDB-package | R package for HITChipDB studies |
| htree.plot | htree.plot |
| import_hitchip | Import HITChip data |
| list.color.scales | List color scales |
| list.mysql.projects | list.mysql.projects |
| mysql.format | Description: Format string vector to mysql query format |
| n.phylotypes.per.oligo | Description: Check number of matching phylotypes for each... |
| oligo.bg.correction | Description: Calculate species summaries and possibly update... |
| phyloarrayConnection | Tests whether the database connection is a phyloarray... |
| phylotype.rm.list | Default list of removed phylotypes and oligos |
| PlotPhylochipHeatmap | PlotPhylochipHeatmap |
| populate.radiobuttons | Description: populate radiobuttons |
| preprocess.chipdata | Description: Profiling preprocessing script |
| prune16S | Description: filter 16S data |
| read_hitchip | Read HITChip |
| ReadParameters | Define parameters in select box |
| ReadPhylogeny | Read phylogeny |
| relative.abundance | Relative abundance |
| retrieve.probesets | retrieve.probesets |
| run.profiling.script | Run profiling script |
| ScaleProfile | Description: Between-arrays normalization |
| scaling.minmax | Description: Minmax scaling. |
| summarize_probedata | Summarize probedata |
| summarize.rawdata | Description: Compress normalized raw data matrix into final... |
| summarize.rpa | Description: Probeset summarization with RPA |
| summarize.sum | Probeset summarization with SUM |
| sync.rm.phylotypes | Description: List oligos associated with removed phylotypes... |
| threshold.data | Description: determine detection threshold for the data |
| WriteChipData | Description: Writed data into the output directory |
| WriteLog | Description: Write log file |
| WriteMatrix | Description: Write matrix in tab file |
