Man pages for ababaian/palmid
Viral RNA Dependent RNA Polymerase Analysis Suite
| fev2df | Convert a palmscan Field-Equals-Value (FEV) column into a... |
| geoFilter | Conversion between run_ids and geo objects often contain... |
| geoFilter2 | Conversion between run_ids and geo objects often contain... |
| get.nickname | get.nickname |
| get.palmSra | A wrapper of several get* functions to create a palm.sra... |
| get.palmTax | get.palmTax |
| get.palmTax2 | get.palmTax2 |
| get.proPhy | Merges 'pro.df' with 'tree.phy' to add annotations from... |
| get.proTax | A wrapper for get.palmTax() specific for 'pro.df' input and... |
| get.proTax2 | A wrapper for get.palmTax() specific for 'pro.df' input and... |
| get.sOTU | get.sOTU |
| get.sra | get.sra |
| get.sraBio | get.sraBio |
| get.sraBio2 | get.sraBio2 |
| get.sraDate | get.sraDate |
| get.sraGeo | get.sraGeo |
| get.sraOrgn | get.sraOrgn |
| get.sraSTAT | get.sraSTAT |
| identityWordcount | identityWordcount |
| linkBLAST | Parse an input sequence into a BLAST-able HTML link |
| linkDB | Parse an input sequence into an Accession-based HTML link |
| linkGB | Parse an input sequence into a GenBank HTML link |
| make_bg_data | Read a multiple-FEV file to create a background set of... |
| normalizeWordcount | normalizeWordCount Create frequency-count table from a set of... |
| palmdb | palmdb |
| PlotDistro | Plot a value relative to a background distribution from a... |
| PlotGeo | A multi-plot wrapper to convert a list of SRA 'run_ids' into... |
| 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... |
| PlotID | Plot Percent-identity vs. E-value of a pro file |
| PlotID2 | Plot Percent-identity vs. GenBank-identity of a pro file |
| PlotLengths | A wrapper for PlotDistro() for "pp_length", "v1_length",... |
| PlotOrgn | Plot a wordcloud of the organisms in a palm.sra object or... |
| PlotOrgnScatter | Plot a scatter-plot of the organisms in a palm.sra object or... |
| PlotPhy | A phylogeny plot wrapper to visualize a phylo object that... |
| PlotPhyBar | A plot wrapper to generate a horizontal bar plot of input... |
| PlotPhyMsa | A multi-plot wrapper to generate an MSA plot from input.msa... |
| PlotPhyReport | A multi-plot wrapper to display a phylogenetic tree of top-10... |
| PlotPP | Plot the palmprint-diagram for a palmscan df object |
| PlotProjExpr | Plot the expression of each palm_id-sra (upto top 10) but... |
| PlotProReport | Create PlotID and PlotTax grid-plot |
| PlotReport | A wrapper for palmid Plot* functions to create a standard... |
| PlotSraExpr | Plot the expression of each palm_id-sra (upto top 10) |
| PlotSTAT | Plot a wordcloud of the STAT-classified taxonomy in a... |
| PlotTax | Plot a taxonomic-classifier based histogram |
| PlotTaxHist | Plot Percent-identity, factored on taxonomic strings of a pro... |
| PlotTaxReport | A multi-plot wrapper to convert a list of SRA 'run_ids' into... |
| PlotTimeline | PlotTimeline Create a timeline of data-releases in palm.sra |
| 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... |
| text_summary | Create a human-readable text summary of palmID |
| waxsys.msa | waxsys.msa |
| waxsys.palmprint | waxsys.palmprint |
| waxsys.palm.sra | waxsys.palm.sra |
| waxsys.pro.df | waxsys.pro.df |
| waxsys.stat.sra | waxsys.stat.sra |
| waxsys.tree.df | waxsys.tree.df |
| waxsys.tree.phy | waxsys.tree.phy |
