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HTSSIP

HTSSIP is an R package for analyzing high throughput sequence data from nucleotide stable isotope probing (DNA- & RNA-SIP) experiments.

Available analyzes

  • Identifying community-level isotope incorporatation

    • Ordinations of gradient fraction communities
    • Beta diversity of overlapping gradient fractions

  • Identifying isotope incorporators

    • High resolution stable isotope probing (HR-SIP)
    • Multiple window high resolution stable isotope probing (MW-HR-SIP)
    • Quantitative stable isotope probing (q-SIP)

Documentation

All documentation can be found on CRAN.

A good place to start is the HTSSIP introduction vignette.

The manuscript describing HTSSIP is:

Youngblut ND, Barnett SE, Buckley DH (2018) HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. PLoS ONE 13(1): e0189616. https://doi.org/10.1371/journal.pone.0189616

References

See References in the HTSSIP introduction vignette.

Installation

To get the current released version from CRAN:

install.packages("HTSSIP")

To get the current development version from github:

# install.packages("devtools")
devtools::install_github("buckleylab/HTSSIP")

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Version

Install

install.packages('HTSSIP')

Monthly Downloads

45

Version

1.4.1

License

GPL-2 | file LICENSE

Maintainer

Samuel Barnett

Last Published

September 13th, 2019

Functions in HTSSIP (1.4.1)

HRSIP

(MW-)HR-SIP analysis
HTSSIP

HTSSIP: analyzing high throughput sequence data from nucleotide stable isotope probing experiments
evaluate_matches

Evaluate String Interpolation Matches
expr_param_extract

Extract all quoted values in the expression used for phyloseq subsetting.
DESeq2_l2fc

Calculating log2 fold change for HTS-SIP data.
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.
fraction_overlap

Calculate the BD range overlap of gradient fractions
HTSSIP_sim

Simulate a HTS-SIP dataset
qSIP_bootstrap

Calculate bootstrap CI for atom fraction excess using q-SIP method
qSIP_atom_excess_format

Reformat a phyloseq object of qSIP_atom_excess analysis
data-physeq_S2D1

(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
calc_atom_excess

Calculate atom fraction excess
phyloseq_list_ord_dfs

Converting ordination objects to data.frames
OTU_qPCR_trans

Transform OTU counts based on qPCR data
phyloseq_ord_plot

Plotting beta diversity ordination
match_brace

Utility Function for Matching a Closing Brace
get_treatment_params

Get parameters for subsetting the phyloseq dataset
calc_Gi

Calculate G+C from unlabeled buoyant density
calc_Mheavymax

Calculate the theoretical maximum molecular weight of fully-labeled DNA
phyloseq_subset

Make a list of phyloseq object subsets
match_placeholders

Match Expression Placeholders for String Interpolation
physeq_format

Checking format of phyloseq object for HTSSIP compatibility
phyloseq2table

Phyloseq conversion to a ggplot-formatted table
tss

Total sum scaling
stringterpolate

String Interpolation
phyloseq2df

phyloseq data object conversion to data.frame
data-physeq_S2D1_l

(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)
data-physeq_rep3_qPCR

(Data) qPCR data associated with the physeq_rep3 HTS-SIP dataset
data-physeq_S2D2

(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
overlap_wmean_dist

Calculating weighted mean beta-diversities of overlapping gradient fractions.
physeq_list_ord

calculating ordinations from a list of distance matrices
heavy_SIP

Heavy-SIP analysis
max_BD_range

Adjusting BD range size if negative.
gradient_sim

Simulate HTS-SIP communities for 1 density gradient
physeq_list_betaDiv

calculating beta diversity for a list of phyloseq objects
delta_BD

delta_BD calculation
format_metadata

Format phyloseq metadata for calculating BD range overlaps.
as.Num

conversion to numeric
SIP_betaDiv_ord

Calculating & plotting beta diversity for a list of phyloseq objects
filter_l2fc

Filter l2fc table
data-physeq_S2D2_l

(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)
qSIP_atom_excess

Calculate atom fraction excess using q-SIP method
qPCR_sim

Simulate qPCR values
data-physeq_rep3

(Data) A simulated HTS-SIP dataset
extract_expressions

Extract Expression Objects from String Interpolation Matches
extract_formats

Extract String Interpolation Formats from Matched Placeholders
perc_overlap

Calculate the percent overlap between two ranges (x & y).
parse_dist

Filtering out non-relevant distances in distance matrix