Package: HTSSIP 1.4.1

HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).

Authors:Nicholas Youngblut [aut], Samuel Barnett [cre, ctb]

HTSSIP_1.4.1.tar.gz
HTSSIP_1.4.1.zip(r-4.5)HTSSIP_1.4.1.zip(r-4.4)HTSSIP_1.4.1.zip(r-4.3)
HTSSIP_1.4.1.tgz(r-4.4-any)HTSSIP_1.4.1.tgz(r-4.3-any)
HTSSIP_1.4.1.tar.gz(r-4.5-noble)HTSSIP_1.4.1.tar.gz(r-4.4-noble)
HTSSIP_1.4.1.tgz(r-4.4-emscripten)HTSSIP_1.4.1.tgz(r-4.3-emscripten)
HTSSIP.pdf |HTSSIP.html✨
HTSSIP/json (API)
NEWS

# Install 'HTSSIP' in R:
install.packages('HTSSIP', repos = c('https://seb369.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/seb369/htssip/issues

Datasets:

On CRAN:

6.58 score 1 packages 40 scripts 342 downloads 4 mentions 25 exports 97 dependencies

Last updated 5 years agofrom:0f3fe86840. Checks:OK: 1 WARNING: 1 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winNOTENov 17 2024
R-4.5-linuxWARNINGNov 17 2024
R-4.4-winNOTENov 17 2024
R-4.4-macNOTENov 17 2024
R-4.3-winNOTENov 17 2024
R-4.3-macNOTENov 17 2024

Exports:as.NumBD_shiftdelta_BDDESeq2_l2fcexpr_param_extractget_treatment_paramsgradient_simheavy_SIPHRSIPHTSSIP_simOTU_qPCR_transphyloseq_list_ord_dfsphyloseq_ord_plotphyloseq_subsetphyloseq2dfphyloseq2tablephyseq_formatphyseq_list_betaDivphyseq_list_ordqPCR_simqSIP_atom_excessqSIP_bootstrapSIP_betaDiv_ordstringterpolatetss

Dependencies:abindade4apeaskpassBHBiobaseBiocGenericsBiocParallelbiomformatBiostringscliclustercodetoolscoenoclinercolorspacecpp11crayoncurldata.tableDelayedArrayDESeq2digestdplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrpurrrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalessnowspSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc

BD shifts

Nick Youngblut

Rendered fromBD_shifts.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2018-05-03
Started: 2016-08-11

Beta diversity ordinations

Nick Youngblut

Rendered frombeta_diversity_ordinations.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2018-05-03
Started: 2016-08-11

heavy-SIP

Nick Youngblut

Rendered fromheavy_SIP.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2018-05-03
Started: 2017-12-20

HTS-SIP data simulation

Nick Youngblut

Rendered fromHTSSIP_sim.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2018-05-03
Started: 2016-08-27

HTSSIP introduction

Nick Youngblut

Rendered fromHTSSIP_intro.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2018-05-03
Started: 2016-08-13

MW-HR-SIP

Nick Youngblut

Rendered fromMW_HR_SIP.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2018-05-03
Started: 2016-08-13

q-SIP

Nick Youngblut

Rendered fromqSIP.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2019-09-13
Started: 2016-08-27

Quantifying isotope incorporation

Nick Youngblut

Rendered fromquant_incorp.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2018-05-03
Started: 2016-08-31

Readme and manuals

Help Manual

Help pageTopics
conversion to numericas.Num
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.BD_shift
Calculate atom fraction excesscalc_atom_excess
Calculate G+C from unlabeled buoyant densitycalc_Gi
Calculate the theoretical maximum molecular weight of fully-labeled DNAcalc_Mheavymax
(Data) A simulated HTS-SIP datasetdata-physeq_rep3 physeq_rep3
(Data) qPCR data associated with the physeq_rep3 HTS-SIP datasetdata-physeq_rep3_qPCR physeq_rep3_qPCR
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)data-physeq_S2D1 physeq_S2D1
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=1)data-physeq_S2D1_l physeq_S2D1_l
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)data-physeq_S2D2 physeq_S2D2
(Data) A subset of full HTS-SIP dataset (Substrates=2, Days=2)data-physeq_S2D2_l physeq_S2D2_l
delta_BD calculationdelta_BD
Calculating log2 fold change for HTS-SIP data.DESeq2_l2fc
Evaluate String Interpolation Matchesevaluate_matches
Extract all quoted values in the expression used for phyloseq subsetting.expr_param_extract
Extract Expression Objects from String Interpolation Matchesextract_expressions
Extract String Interpolation Formats from Matched Placeholdersextract_formats
Filter l2fc tablefilter_l2fc
Format phyloseq metadata for calculating BD range overlaps.format_metadata
Calculate the BD range overlap of gradient fractionsfraction_overlap
Get parameters for subsetting the phyloseq datasetget_treatment_params
Simulate HTS-SIP communities for 1 density gradientgradient_sim
Heavy-SIP analysisheavy_SIP
(MW-)HR-SIP analysisHRSIP
HTSSIP: analyzing high throughput sequence data from nucleotide stable isotope probing experimentsHTSSIP-package HTSSIP
Simulate a HTS-SIP datasetHTSSIP_sim
Utility Function for Matching a Closing Bracematch_brace
Match Expression Placeholders for String Interpolationmatch_placeholders
Adjusting BD range size if negative.max_BD_range
Transform OTU counts based on qPCR dataOTU_qPCR_trans
Calculating weighted mean beta-diversities of overlapping gradient fractions.overlap_wmean_dist
Filtering out non-relevant distances in distance matrixparse_dist
Calculate the percent overlap between two ranges (x & y).perc_overlap
Converting ordination objects to data.framesphyloseq_list_ord_dfs
Plotting beta diversity ordinationphyloseq_ord_plot
Make a list of phyloseq object subsetsphyloseq_subset
phyloseq data object conversion to data.framephyloseq2df
Phyloseq conversion to a ggplot-formatted tablephyloseq2table
Checking format of phyloseq object for HTSSIP compatibilityphyseq_format
calculating beta diversity for a list of phyloseq objectsphyseq_list_betaDiv
calculating ordinations from a list of distance matricesphyseq_list_ord
Simulate qPCR valuesqPCR_sim
Calculate atom fraction excess using q-SIP methodqSIP_atom_excess
Reformat a phyloseq object of qSIP_atom_excess analysisqSIP_atom_excess_format
Calculate bootstrap CI for atom fraction excess using q-SIP methodqSIP_bootstrap
Calculating & plotting beta diversity for a list of phyloseq objectsSIP_betaDiv_ord
String Interpolationstringterpolate
Total sum scalingtss