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 |
heavy_SIP |
Heavy-SIP analysis |
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 |