Package: omicsTools 1.1.2

Yaoxiang Li

omicsTools: Omics Data Process Toolbox

Processing and analyzing omics data from genomics, transcriptomics, proteomics, and metabolomics platforms. It provides functions for preprocessing, normalization, visualization, and statistical analysis, as well as machine learning algorithms for predictive modeling. 'omicsTools' is an essential tool for researchers working with high-throughput omics data in fields such as biology, bioinformatics, and medicine.The QC-RLSC (quality control–based robust LOESS signal correction) algorithm is used for normalization. Dunn et al. (2011) <doi:10.1038/nprot.2011.335>.

Authors:Yaoxiang Li [cre, aut], Meth Jayatilake [aut], Zihao Zhang [aut], Amrita Cheema [aut]

omicsTools_1.1.2.tar.gz
omicsTools_1.1.2.zip(r-4.5)omicsTools_1.1.2.zip(r-4.4)omicsTools_1.1.2.zip(r-4.3)
omicsTools_1.1.2.tgz(r-4.4-any)omicsTools_1.1.2.tgz(r-4.3-any)
omicsTools_1.1.2.tar.gz(r-4.5-noble)omicsTools_1.1.2.tar.gz(r-4.4-noble)
omicsTools_1.1.2.tgz(r-4.4-emscripten)omicsTools_1.1.2.tgz(r-4.3-emscripten)
omicsTools.pdf |omicsTools.html✨
omicsTools/json (API)
NEWS

# Install 'omicsTools' in R:

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

The latest version of this package failed to build. Look at thebuild logs for more information.

Bug tracker:https://github.com/yaoxiangli/omicstools/issues

On CRAN:

25 exports 1 stars 1.59 score 100 dependencies 7 scripts 159 downloads

Last updated 3 months agofrom:3e1e4f8692. Checks:OK: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Jun 19 2024

Exports:%>%calculate_cooks_distance calculate_lof calculate_measures convert_to_binary_matrix createOmicsData define_thresholds ensure_enough_sets_for_upset flag_anomalies generate_data_with_anomalies handle_missing_values initialize_results_df is_normalize load_is_area load_peak_area nist_rsd pieDraw plot_distribution_measures plot_sample_measures prepare_upset_data pvcaBF pvcaDraw qc_normalize qc_rsd run_app

Dependencies:askpass attempt base64enc bit bit64 bs4Dash bslib cachem cli clipr colorspace commonmark config cpp11 crayon crosstalk curl dbscan digest dplyr DT evaluate fansi farver fastmap fontawesome fresh fs generics ggplot2 glue golem gridExtra gtable here highr hms htmltools htmlwidgets httpuv httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime moments munsell nlme openssl outliers pillar pkgconfig plyr prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown rprojroot rstudioapi sass scales shiny sourcetools stringi stringr sys tibble tidyr tidyselect tinytex tzdb UpSetR utf8 vctrs viridisLite vroom waiter withr xfun xtable yaml

OmicsData Example Usage

Rendered fromexample_usage.Rmdusingknitr::rmarkdownon Jun 19 2024.

Last update: 2024-06-10
Started: 2024-06-10

Help page	Topics
Calculate Cook's Distance	calculate_cooks_distance
Calculate Local Outlier Factor (LOF)	calculate_lof
Calculate Measures for Each Feature	calculate_measures
Convert to Binary Matrix for UpSetR	convert_to_binary_matrix
Constructor for OmicsData	createOmicsData
Define Anomaly Thresholds	define_thresholds
Ensure There Are Enough Sets for UpSet Plot	ensure_enough_sets_for_upset
Flag Anomalies	flag_anomalies
Generate High-Dimensional Data with Anomalies	generate_data_with_anomalies
Handle Missing Values in a Tibble	handle_missing_values
Initialize Results Data Frame	initialize_results_df
Normalize loaded tibble with IS tibble	is_normalize
Load and clean IS area data	load_is_area
Load and clean peak area data	load_peak_area
Calculate the relative standard deviation for NIST samples	nist_rsd
OmicsData Class	OmicsData-class
import ggplot2	pieDraw
Plot Distribution Measures	plot_distribution_measures
Plot Sample Measures	plot_sample_measures
Prepare Data for UpSet Plot	prepare_upset_data
import Biobase pcva	pvcaBF
import ggplot2	pvcaDraw
QC-Normalize function	qc_normalize
Calculate the relative standard deviation for QC samples	qc_rsd
Run the Shiny Application	run_app

Package: omicsTools 1.1.2

omicsTools: Omics Data Process Toolbox

OmicsData Example Usage

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Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)