High Throughput Sequencing of Stable Isotope Probing Data Analysis
conversion to numeric
Assessing the magnitude of BD shifts with 16S rRNA community data by c...
Calculate atom fraction excess
Calculate G+C from unlabeled buoyant density
Calculate the theoretical maximum molecular weight of fully-labeled DN...
(Data) A simulated HTS-SIP dataset
(Data) qPCR data associated with the physeq_rep3 HTS-SIP dataset
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
delta_BD calculation
Calculating log2 fold change for HTS-SIP data.
Evaluate String Interpolation Matches
Extract all quoted values in the expression used for phyloseq subsetti...
Extract Expression Objects from String Interpolation Matches
Extract String Interpolation Formats from Matched Placeholders
Filter l2fc table
Format phyloseq metadata for calculating BD range overlaps.
Calculate the BD range overlap of gradient fractions
Get parameters for subsetting the phyloseq dataset
Simulate HTS-SIP communities for 1 density gradient
Heavy-SIP analysis
(MW-)HR-SIP analysis
HTSSIP: analyzing high throughput sequence data from nucleotide stable...
Simulate a HTS-SIP dataset
Utility Function for Matching a Closing Brace
Match Expression Placeholders for String Interpolation
Adjusting BD range size if negative.
Transform OTU counts based on qPCR data
Calculating weighted mean beta-diversities of overlapping gradient fra...
Filtering out non-relevant distances in distance matrix
Calculate the percent overlap between two ranges (x & y).
Converting ordination objects to data.frames
Plotting beta diversity ordination
Make a list of phyloseq object subsets
phyloseq data object conversion to data.frame
Phyloseq conversion to a ggplot-formatted table
Checking format of phyloseq object for HTSSIP compatibility
calculating beta diversity for a list of phyloseq objects
calculating ordinations from a list of distance matrices
Simulate qPCR values
Calculate atom fraction excess using q-SIP method
Reformat a phyloseq object of qSIP_atom_excess analysis
Calculate bootstrap CI for atom fraction excess using q-SIP method
Calculating & plotting beta diversity for a list of phyloseq objects
String Interpolation
Total sum scaling
Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).