Package: SIPmg 2.3

Pranav Sampara

SIPmg: Statistical Analysis to Identify Isotope Incorporating metagenomic features

Statistical analysis as part of a quantitative stable isotope probing (SIP) metagenomics study to identify isotope incorporating metagenomic features. Helpful reading and a vignette in bookdown format is provided on the package site <https://zielslab.github.io/SIPmg.github.io/>.

Authors:Pranav Sampara [aut, cre], Kate Waring [ctb], Ryan Ziels [aut], Alma Garcia Roche [aut]

SIPmg_2.3.tar.gz
SIPmg_2.3.zip(r-4.5)SIPmg_2.3.zip(r-4.4)SIPmg_2.3.zip(r-4.3)
SIPmg_2.3.tgz(r-4.4-any)SIPmg_2.3.tgz(r-4.3-any)
SIPmg_2.3.tar.gz(r-4.5-noble)SIPmg_2.3.tar.gz(r-4.4-noble)
SIPmg_2.3.tgz(r-4.4-emscripten)SIPmg_2.3.tgz(r-4.3-emscripten)
SIPmg.pdf |SIPmg.html✨
SIPmg/json (API)

# Install 'SIPmg' in R:

install.packages('SIPmg', repos = c('https://zielslab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zielslab/sipmg/issues

Datasets:

GC_content - GC_content table
atomX - Atom fraction excess table
df_atomX_boot - Bootstrapped atom fraction excess table
f_tibble - Coverage table
fractions - Fractions table
mag.table - MAG abundance table in phyloseq format
phylo.qSIP - Master phyloseq object
samples.object - Fractions table in phyloseq format
seq_dil - Sequins dilution table
sequins - Sequins table
taxonomy.object - Taxonomy table in phyloseq format
taxonomy_tibble - Taxonomy table

On CRAN:

3.78 score 9 scripts 222 downloads 12 exports 127 dependencies

Last updated 4 months agofrom:173d42ba75. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Oct 13 2024
R-4.5-win	WARNING	Oct 13 2024
R-4.5-linux	WARNING	Oct 13 2024
R-4.4-win	WARNING	Oct 13 2024
R-4.4-mac	WARNING	Oct 13 2024
R-4.3-win	WARNING	Oct 13 2024
R-4.3-mac	WARNING	Oct 13 2024

Exports:coverage_normalization DESeq2_l2fc filter_na HRSIP incorporators_taxonomy phylo.table qSIP_atom_excess_MAGs qSIP_bootstrap_fcr sample.table scale_features_lm scale_features_rlm tax.table

Dependencies:abind ade4 ape askpass backports BH Biobase BiocGenerics BiocParallel biomformat Biostrings boot broom car carData cli cluster codetools coenocliner colorspace corrplot cowplot cpp11 crayon curl data.table DelayedArray Deriv DESeq2 digest doBy dplyr fansi farver foreach formatR Formula futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable HTSSIP httr igraph IRanges isoband iterators jsonlite labeling lambda.r lattice lazyeval lifecycle lme4 locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv microbenchmark mime minqa modelr multtest munsell nlme nloptr nnet numDeriv openssl pbkrtest permute phyloseq pillar pixmap pkgconfig plyr polynom purrr quantreg R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rstatix S4Arrays S4Vectors scales snow sp SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs vegan viridisLite withr XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Atom fraction excess table	atomX
Calculate atom fraction excess	calc_atom_excess_MAGs
Calculate Mheavymax	calc_Mheavymax_MAGs
Normalize feature coverages to estimate absolute abundance or relative coverage using MAG/contig coverage values with or without multiplying total DNA concentration of the fraction	coverage_normalization
Calculating log2 fold change for HTS-SIP data.	DESeq2_l2fc
Bootstrapped atom fraction excess table	df_atomX_boot
Coverage table	f_tibble
Filter l2fc table	filter_l2fc
Remove MAGs with NAs from atomX table	filter_na
Fractions table	fractions
GC_content table	GC_content
(MW-)HR-SIP analysis	HRSIP
Isotope incorporator list with GTDB taxonomy	incorporators_taxonomy
MAG abundance table in phyloseq format	mag.table
Master phyloseq object	phylo.qSIP
Master phyloseq object using the MAG phyloseq objects	phylo.table
Reformat a phyloseq object of qSIP_atom_excess_MAGs analysis	qSIP_atom_excess_format_MAGs
Calculate atom fraction excess using q-SIP method	qSIP_atom_excess_MAGs
Calculate adjusted bootstrap CI after for multiple testing for atom fraction excess using q-SIP method. Multiple hypothesis tests are corrected by	qSIP_bootstrap_fcr
phyloseq-styled sample table	sample.table
Fractions table in phyloseq format	samples.object
Scale feature coverage values to estimate their absolute abundance	scale_features_lm
Scale feature coverage values to estimate their absolute abundance	scale_features_rlm
Sequins dilution table	seq_dil
Sequins table	sequins
phyloseq taxa table from GTDB taxonomy input	tax.table
Taxonomy table	taxonomy_tibble
Taxonomy table in phyloseq format	taxonomy.object