Package: demic 2.0.0.9000

demic: Dynamic Estimator of Microbial Communities

Multi-sample algorithm based on contigs and coverage values, to infer the relative distances of contigs from the replication origin and to accurately compare bacterial growth rates between samples. Yuan Gao and Hongzhe Li (2018) <doi:10.1038/s41592-018-0182-0>.

Authors:Yuan Gao [aut, cph], Charlie Bushman [cre]

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demic.pdf |demic.html✨
demic/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/ulthran/demic/issues

Datasets:

On CRAN:

4 exports 1.52 score 20 dependencies 3 scripts 168 downloads

Last updated 8 months agofrom:be8c0c0902. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 22 2024
R-4.5-winNOTEAug 22 2024
R-4.5-linuxNOTEAug 22 2024
R-4.4-winNOTEAug 22 2024
R-4.4-macNOTEAug 22 2024
R-4.3-winNOTEAug 22 2024
R-4.3-macNOTEAug 22 2024

Exports:est_ptrest_ptr_onest_ptr_on_allget_eptr_stats

Dependencies:bootcligluelatticelifecyclelme4magrittrMASSMatrixminqanlmenloptrplyrRcppRcppEigenreshape2rlangstringistringrvctrs

Readme and manuals

Help Manual

Help pageTopics
Compares contig subset x against contig subset ycompare_contig_subsets
Compares sample subset x against sample subset ycompare_sample_subsets
A function for data frame integrationconsist_transfer
A function to return the first dimension of PCA on an input matrixcontig_pca
Contig Cluster 1ContigCluster1
Contig Cluster 2ContigCluster2
Determine the majority orientation of the input PTR estimates correlationscor_diff
A function for data frame transferdf_transfer
Estimate PTRs using all input data as well as using subsets of contigs and samplesest_ptr
Tries up to max_attempts times to compare each permutation of removing random subsets of contigs/samples from X, and returns the PTR estimate if a valid one comes back from the comparisonsest_ptr_on
Estimates PTRs based on the whole input datasetest_ptr_on_all
Get PTR estimates for output of the core pipeline on a subset of dataest_ptrs_subset
A function for sample filtration Input requirements: 1. have values in more than half of the contigs 2. average log2(cov) > 0 in all these contigsfilter_sample
Generate a variety of stats on PTR estimates for a given datasetget_eptr_stats
A function for iteration of pipeline until convergenceiterate_pipelines
A convenient function for KS test of uniform distributionks
A convenient function for ordinary linear regression on two vectorslm_column
Run mixed linear model with random effect using lme4lme4_model
MaxBin2 Cluster 001max_bin_001
MaxBin2 Cluster 002max_bin_002
MaxBin2 Cluster 003max_bin_003
A function representing the pipeline of four steps including GC bias correction, sample filtration, PCA and contig filtrationpipeline
A function for reshape to facilitate PCA, removing all contigs with missing values for designated samplesreshape_filtered
A function to remove outlier contigs using KS testselect_by_ks_test
A function to test whether the result is reasonabletest_reasonable
Verify that the input dataframe/matrix is validverify_input