Package: rKOMICS 1.2

Manon Geerts

rKOMICS: Minicircle Sequence Cluster (MSC) Analyses

It establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history.

Authors:Frederik Van den Broeck [aut], Manon Geerts [aut, cre]

rKOMICS_1.2.tar.gz
rKOMICS_1.2.zip(r-4.5)rKOMICS_1.2.zip(r-4.4)rKOMICS_1.2.zip(r-4.3)
rKOMICS_1.2.tgz(r-4.4-any)rKOMICS_1.2.tgz(r-4.3-any)
rKOMICS_1.2.tar.gz(r-4.5-noble)rKOMICS_1.2.tar.gz(r-4.4-noble)
rKOMICS_1.2.tgz(r-4.4-emscripten)rKOMICS_1.2.tgz(r-4.3-emscripten)
rKOMICS.pdf |rKOMICS.html✨
rKOMICS/json (API)

# Install 'rKOMICS' in R:

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

Bug tracker:https://github.com/geertsmanon/rkomics/issues

Datasets:

exData - Example dataset
matrices - Example cluster matrices

On CRAN:

3.00 score 2 scripts 202 downloads 1 mentions 14 exports 129 dependencies

Last updated 3 years agofrom:a51234afd2. Checks:OK: 1 WARNING: 1 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 10 2024
R-4.5-win	NOTE	Nov 10 2024
R-4.5-linux	WARNING	Nov 10 2024
R-4.4-win	NOTE	Nov 10 2024
R-4.4-mac	NOTE	Nov 10 2024
R-4.3-win	NOTE	Nov 10 2024
R-4.3-mac	NOTE	Nov 10 2024

Exports:%>%msc.depth msc.heatmap msc.length msc.matrix msc.pca msc.quality msc.richness msc.seqs msc.similarity msc.subset msc.uc preprocess read.uc

Dependencies:abind ape backports base64enc BiocGenerics boot broom bslib cachem car carData circlize cli clue cluster codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon crosstalk dendextend Deriv digest doBy doParallel dplyr DT ellipse emmeans estimability evaluate factoextra FactoMineR fansi farver fastmap flashClust fontawesome foreach Formula fs generics GetoptLong ggplot2 ggpubr ggrepel ggsci ggsignif GlobalOptions glue gridExtra gtable highr htmltools htmlwidgets httpuv IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval leaps lifecycle lme4 magrittr MASS Matrix MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr multcompView munsell mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plyr png polynom promises purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rjson rlang rmarkdown rstatix S4Vectors sass scales scatterplot3d shape SparseM stringi stringr survival tibble tidyr tidyselect tinytex utf8 vctrs viridis viridisLite withr xfun yaml

Application example

Rendered fromexample.Rnwusingutils::Sweaveon Nov 10 2024.

Last update: 2021-09-12
Started: 2021-09-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example dataset	exData
Example cluster matrices	matrices
Check the read depth of assembled minicircles	msc.depth
Visualization of cluster matrices	msc.heatmap
Length of minicircles	msc.length
Build cluster matrix	msc.matrix
Prinicple Component Analysis based on MSC	msc.pca
Check the quality of the assembly	msc.quality
Minicircle Sequence Cluster richness	msc.richness
Retrieve sequences	msc.seqs
Minicircle Sequence Cluster similarity	msc.similarity
Specific MSC	msc.subset
Cluster Analyses	msc.uc
Filtering of minicircle sequences	preprocess
Read in uc files	read.uc
Minicircle Sequence Cluster (MSC) Analyses	rKOMICS