# High Throughput Sequencing of Stable Isotope Probing Data Analysis

## Documentation for package ‘HTSSIP’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

HTSSIP-package | HTSSIP: analyzing high throughput sequence data from nucleotide stable isotope probing experiments
as.Num | conversion to numeric
BD_shift | Assessing the magnitude of BD shifts with 16S rRNA community data by calculating the beta diversity between unlabeled control and labeled treatment gradient fraction communities.
calc_atom_excess | Calculate atom fraction excess
calc_Gi | Calculate G+C from unlabeled buoyant density
calc_Mheavymax | Calculate the theoretical maximum molecular weight of fully-labeled DNA
data-physeq_rep3 | (Data) A simulated HTS-SIP dataset
data-physeq_rep3_qPCR | (Data) qPCR data associated with the physeq_rep3 HTS-SIP dataset
data-physeq_S2D1 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
data-physeq_S2D1_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
data-physeq_S2D2 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
data-physeq_S2D2_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
delta_BD | delta_BD calculation
DESeq2_l2fc | Calculating log2 fold change for HTS-SIP data.
evaluate_matches | Evaluate String Interpolation Matches
expr_param_extract | Extract all quoted values in the expression used for phyloseq subsetting.
extract_expressions | Extract Expression Objects from String Interpolation Matches
extract_formats | Extract String Interpolation Formats from Matched Placeholders
filter_l2fc | Filter l2fc table
format_metadata | Format phyloseq metadata for calculating BD range overlaps.
fraction_overlap | Calculate the BD range overlap of gradient fractions
get_treatment_params | Get parameters for subsetting the phyloseq dataset
gradient_sim | Simulate HTS-SIP communities for 1 density gradient
HRSIP | (MW-)HR-SIP analysis
HTSSIP | HTSSIP: analyzing high throughput sequence data from nucleotide stable isotope probing experiments
HTSSIP_sim | Simulate a HTS-SIP dataset
match_brace | Utility Function for Matching a Closing Brace
match_placeholders | Match Expression Placeholders for String Interpolation
max_BD_range | Adjusting BD range size if negative.
OTU_qPCR_trans | Transform OTU counts based on qPCR data
overlap_wmean_dist | Calculating weighted mean beta-diversities of overlapping gradient fractions.
parse_dist | Filtering out non-relevant distances in distance matrix
perc_overlap | Calculate the percent overlap between two ranges (x & y).
phyloseq2df | phyloseq data object conversion to data.frame
phyloseq2table | Phyloseq conversion to a ggplot-formatted table
phyloseq_list_ord_dfs | Converting ordination objects to data.frames
phyloseq_ord_plot | Plotting beta diversity ordination
phyloseq_subset | Make a list of phyloseq object subsets
physeq_format | Checking format of phyloseq object for HTSSIP compatibility
physeq_list_betaDiv | calculating beta diversity for a list of phyloseq objects
physeq_list_ord | calculating ordinations from a list of distance matrices
physeq_rep3 | (Data) A simulated HTS-SIP dataset
physeq_rep3_qPCR | (Data) qPCR data associated with the physeq_rep3 HTS-SIP dataset
physeq_S2D1 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
physeq_S2D1_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
physeq_S2D2 | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
physeq_S2D2_l | (Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
qPCR_sim | Simulate qPCR values
qSIP_atom_excess | Calculate atom fraction excess using q-SIP method
qSIP_atom_excess_format | Reformat a phyloseq object of qSIP_atom_excess analysis
qSIP_bootstrap | Calculate bootstrap CI for atom fraction excess using q-SIP method
SIP_betaDiv_ord | Calculating & plotting beta diversity for a list of phyloseq objects
stringterpolate | String Interpolation
tss | Total sum scaling