HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Perform HTS-SIP analyses such as high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP). More information on HR-SIP, MW-HR-SIP, and q-SIP can be found in: 1) Pepe-Ranney, Charles, Ashley N. Campbell, Chantal N. Koechli, Sean Berthrong, and Daniel H. Buckley. 2016. "Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil." Terrestrial Microbiology, 703. <doi:10.3389/fmicb.2016.00703> 2) Youngblut, Nicholas D., and Daniel H. Buckley. "Evaluating the Accuracy of DNA Stable Isotope Probing". in prep. 3) Hungate, Bruce A., Rebecca L. Mau, Egbert Schwartz, J. Gregory Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J. Koch, et al. 2015. "Quantitative Microbial Ecology Through Stable Isotope Probing." Applied and Environmental Microbiology, August, AEM.02280-15. <doi:10.1128/AEM.02280-15>

Install the latest version of this package by entering the following in R:
install.packages("HTSSIP")
AuthorNicholas Youngblut [aut, cre], Samuel Barnett [ctb]
Date of publication2016-11-01 23:06:54
MaintainerNicholas Youngblut <nyoungb2@gmail.com>
LicenseGPL-2 | file LICENSE
Version1.0.3

View on CRAN

Man pages

as.Num: conversion to numeric

BD_shift: Assessing the magnitude of BD shifts with 16S rRNA community...

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...

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_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...

extract_expressions: Extract Expression Objects from String Interpolation Matches

extract_formats: Extract String Interpolation Formats from Matched...

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...

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...

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

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...

SIP_betaDiv_ord: Calculating & plotting beta diversity for a list of phyloseq...

stringterpolate: String Interpolation

tss: Total sum scaling

Functions

as.Num Man page
BD_shift Man page
calc_atom_excess Man page
calc_Gi Man page
calc_Mheavymax Man page
data-physeq_rep3 Man page
data-physeq_rep3_qPCR Man page
data-physeq_S2D1 Man page
data-physeq_S2D1_l Man page
data-physeq_S2D2 Man page
data-physeq_S2D2_l Man page
delta_BD Man page
DESeq2_l2fc Man page
evaluate_matches Man page
expr_param_extract Man page
extract_expressions Man page
extract_formats Man page
filter_l2fc Man page
format_metadata Man page
fraction_overlap Man page
get_treatment_params Man page
gradient_sim Man page
HRSIP Man page
HTSSIP Man page
HTSSIP-package Man page
HTSSIP_sim Man page
match_brace Man page
match_placeholders Man page
max_BD_range Man page
OTU_qPCR_trans Man page
overlap_wmean_dist Man page
parse_dist Man page
perc_overlap Man page
phyloseq2df Man page
phyloseq2table Man page
phyloseq_list_ord_dfs Man page
phyloseq_ord_plot Man page
phyloseq_subset Man page
physeq_format Man page
physeq_list_betaDiv Man page
physeq_list_ord Man page
physeq_rep3 Man page
physeq_rep3_qPCR Man page
physeq_S2D1 Man page
physeq_S2D1_l Man page
physeq_S2D2 Man page
physeq_S2D2_l Man page
qPCR_sim Man page
qSIP_atom_excess Man page
qSIP_atom_excess_format Man page
qSIP_bootstrap Man page
SIP_betaDiv_ord Man page
stringterpolate Man page
tss Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/beta_diversity_ordinations.Rmd
inst/doc/BD_shifts.R inst/doc/quant_incorp.R
inst/doc/quant_incorp.html
inst/doc/MW_HR_SIP.R
inst/doc/quant_incorp.Rmd
inst/doc/HTSSIP_intro.html
inst/doc/beta_diversity_ordinations.html
inst/doc/BD_shifts.html
inst/doc/HTSSIP_sim.html
inst/doc/qSIP.html
inst/doc/MW_HR_SIP.html
inst/doc/beta_diversity_ordinations.R
inst/doc/BD_shifts.Rmd
inst/doc/HTSSIP_intro.Rmd
inst/doc/qSIP.R
inst/doc/qSIP.Rmd
inst/doc/HTSSIP_sim.Rmd
inst/doc/HTSSIP_sim.R inst/doc/HTSSIP_intro.R
inst/doc/MW_HR_SIP.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-HRSIP.R tests/testthat/test-BD_ordinations.R tests/testthat/test-stringterpolate.R tests/testthat/test-qSIP_atom_excess.R tests/testthat/test-HTSSIP_sim.R tests/testthat/test-DESeq2_l2fc.R tests/testthat/test-chk.R tests/testthat/test-delta_BD.R tests/testthat/test-phyloseq_subset.R tests/testthat/test-Util.R tests/testthat/test-qSIP_trans.R tests/testthat/test-qPCR.R tests/testthat/test-BD_shift.R
NAMESPACE
NEWS.md
data
data/physeq_rep3_qPCR.rda
data/physeq_S2D2_l.rda
data/physeq_S2D1.rda
data/physeq_S2D1_l.rda
data/physeq_rep3.rda
data/datalist
data/physeq_S2D2.rda
R
R/stringterpolate.R R/BD_shift.R R/HRSIP.R R/pkg_data.R R/HTSSIP.R R/Util.R R/qSIP_trans.R R/DESeq2_l2fc.R R/phyloseq_subset.R R/BD_ordinations.R R/chk.R R/delta_BD.R R/HTSSIP_sim.R R/qPCR.R R/qSIP_atom_excess.R
vignettes
vignettes/beta_diversity_ordinations.Rmd
vignettes/quant_incorp.Rmd
vignettes/BD_shifts.Rmd
vignettes/HTSSIP_intro.Rmd
vignettes/qSIP.Rmd
vignettes/HTSSIP_sim.Rmd
vignettes/MW_HR_SIP.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/DESeq2_l2fc.Rd man/calc_Mheavymax.Rd man/delta_BD.Rd man/qSIP_atom_excess.Rd man/expr_param_extract.Rd man/get_treatment_params.Rd man/calc_atom_excess.Rd man/physeq_list_ord.Rd man/qSIP_atom_excess_format.Rd man/filter_l2fc.Rd man/data-physeq_S2D2.Rd man/physeq_list_betaDiv.Rd man/HRSIP.Rd man/data-physeq_rep3.Rd man/data-physeq_S2D1_l.Rd man/overlap_wmean_dist.Rd man/tss.Rd man/max_BD_range.Rd man/phyloseq2df.Rd man/phyloseq_ord_plot.Rd man/qSIP_bootstrap.Rd man/extract_expressions.Rd man/as.Num.Rd man/match_brace.Rd man/OTU_qPCR_trans.Rd man/phyloseq_list_ord_dfs.Rd man/BD_shift.Rd man/format_metadata.Rd man/phyloseq2table.Rd man/SIP_betaDiv_ord.Rd man/phyloseq_subset.Rd man/calc_Gi.Rd man/evaluate_matches.Rd man/HTSSIP.Rd man/perc_overlap.Rd man/match_placeholders.Rd man/data-physeq_rep3_qPCR.Rd man/data-physeq_S2D2_l.Rd man/extract_formats.Rd man/fraction_overlap.Rd man/data-physeq_S2D1.Rd man/parse_dist.Rd man/stringterpolate.Rd man/gradient_sim.Rd man/HTSSIP_sim.Rd man/physeq_format.Rd man/qPCR_sim.Rd
LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.