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>

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

Files in this package

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

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