| fev2df |
Convert a palmscan Field-Equals-Value (FEV) column into a dataframe |
| geoFilter |
Conversion between run_ids and geo objects often contain NA/NULL values This removes NA-containing rows |
| geoFilter2 |
Conversion between run_ids and geo objects often contain NA/NULL values This removes NA-containing rows |
| get.palmSra |
A wrapper of several get* functions to create a palm.sra data.frame |
| get.proTax |
A wrapper for get.tax() specific for 'pro.df' input and returns a populated the "tspe", "tfam", and "tphy" columns of 'pro.df' based on the "sseqid" column |
| get.sOTU |
get.sOTU |
| get.sra |
get.sra |
| get.sraBio |
get.sraBio |
| get.sraDate |
get.sraDate |
| get.sraGeo |
get.sraGeo |
| get.sraOrgn |
get.sraOrgn |
| get.tax |
get.tax |
| identityWordcount |
identityWordcount |
| linkBLAST |
Parse an input sequence into a BLAST-able HTML link |
| make_bg_data |
Read a multiple-FEV file to create a background set of palmprints Standard approach is to use palmDB |
| normalizeWordcount |
normalizeWordCount Create frequency-count table from a set of characters which are normalized as percentage of total corpus |
| palmdb |
palmdb |
| PlotDistro |
Plot a value relative to a background distribution from a palmprint data.frame. |
| PlotGeo |
A multi-plot wrapper to convert a list of SRA 'run_ids' into a geographic world-map and timeline. |
| PlotGeo2 |
Create a rich plotly geo map from a palm.sra data.frame |
| PlotGeoReport |
A multi-plot wrapper to convert a list of SRA 'run_ids' into a geographic world-map and timeline. |
| PlotID |
Plot Percent-identity vs. E-value of a pro file |
| PlotLengths |
A wrapper for PlotDistro() for "pp_length", "v1_length", "v2_length". |
| PlotOrgn |
Plot a wordcloud of the organisms in a palm.sra object or orgn.vec |
| PlotPP |
Plot the palmprint-diagram for a palmscan df object |
| PlotProReport |
Create PlotID and PlotTax grid-plot |
| PlotReport |
A wrapper for palmid Plot* functions to create a standard "report" |
| PlotTax |
Plot a taxonomic-classifier based histogram |
| PlotTaxHist |
Plot Percent-identity, factored on taxonomic strings of a pro df |
| PlotTaxReport |
A multi-plot wrapper to convert a list of SRA 'run_ids' into a geographic world-map and timeline. |
| PlotTimeline |
PlotTimeline Create a timeline of |
| read.fev |
Reads a .fev file created by 'palmscan' |
| read.pro |
Reads a .pro file created by 'diamond' |
| SerratusConnect |
SerratusConnect |
| standardizeWordcount |
standardizeWordcount Create frequency-count table from a set of characters which are assigned a standardized rank-order scores from 10.0 to 1.0. |
| waxsys.palm.sra |
waxsys.palm.sra |
| waxsys.palmprint |
waxsys.palmprint |
| waxsys.pro.df |
waxsys.pro.df |
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