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>

Author
Nicholas Youngblut [aut, cre], Samuel Barnett [ctb]
Date of publication
2016-11-01 23:06:54
Maintainer
Nicholas Youngblut <nyoungb2@gmail.com>
License
GPL-2 | file LICENSE
Version
1.0.3

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