Man pages for HTSSIP
High Throughput Sequencing of Stable Isotope Probing Data Analysis

as.Numconversion to numeric
BD_shiftAssessing the magnitude of BD shifts with 16S rRNA community...
calc_atom_excessCalculate atom fraction excess
calc_GiCalculate G+C from unlabeled buoyant density
calc_MheavymaxCalculate the theoretical maximum molecular weight of...
data-physeq_rep3(Data) A simulated HTS-SIP dataset
data-physeq_rep3_qPCR(Data) qPCR data associated with the physeq_rep3 HTS-SIP...
data-physeq_S2D1(Data) A subset of full HTS-SIP dataset (Substrates=2,...
data-physeq_S2D1_l(Data) A subset of full HTS-SIP dataset (Substrates=2,...
data-physeq_S2D2(Data) A subset of full HTS-SIP dataset (Substrates=2,...
data-physeq_S2D2_l(Data) A subset of full HTS-SIP dataset (Substrates=2,...
delta_BDdelta_BD calculation
DESeq2_l2fcCalculating log2 fold change for HTS-SIP data.
evaluate_matchesEvaluate String Interpolation Matches
expr_param_extractExtract all quoted values in the expression used for phyloseq...
extract_expressionsExtract Expression Objects from String Interpolation Matches
extract_formatsExtract String Interpolation Formats from Matched...
filter_l2fcFilter l2fc table
format_metadataFormat phyloseq metadata for calculating BD range overlaps.
fraction_overlapCalculate the BD range overlap of gradient fractions
get_treatment_paramsGet parameters for subsetting the phyloseq dataset
gradient_simSimulate HTS-SIP communities for 1 density gradient
heavy_SIPHeavy-SIP analysis
HRSIP(MW-)HR-SIP analysis
HTSSIPHTSSIP: analyzing high throughput sequence data from...
HTSSIP_simSimulate a HTS-SIP dataset
match_braceUtility Function for Matching a Closing Brace
match_placeholdersMatch Expression Placeholders for String Interpolation
max_BD_rangeAdjusting BD range size if negative.
OTU_qPCR_transTransform OTU counts based on qPCR data
overlap_wmean_distCalculating weighted mean beta-diversities of overlapping...
parse_distFiltering out non-relevant distances in distance matrix
perc_overlapCalculate the percent overlap between two ranges (x & y).
phyloseq2dfphyloseq data object conversion to data.frame
phyloseq2tablePhyloseq conversion to a ggplot-formatted table
phyloseq_list_ord_dfsConverting ordination objects to data.frames
phyloseq_ord_plotPlotting beta diversity ordination
phyloseq_subsetMake a list of phyloseq object subsets
physeq_formatChecking format of phyloseq object for HTSSIP compatibility
physeq_list_betaDivcalculating beta diversity for a list of phyloseq objects
physeq_list_ordcalculating ordinations from a list of distance matrices
qPCR_simSimulate qPCR values
qSIP_atom_excessCalculate atom fraction excess using q-SIP method
qSIP_atom_excess_formatReformat a phyloseq object of qSIP_atom_excess analysis
qSIP_bootstrapCalculate bootstrap CI for atom fraction excess using q-SIP...
SIP_betaDiv_ordCalculating & plotting beta diversity for a list of phyloseq...
stringterpolateString Interpolation
tssTotal sum scaling
HTSSIP documentation built on Sept. 14, 2019, 1:02 a.m.