Package: noisyr 1.1.0

Ilias Moutsopoulos

noisyr: Noise Quantification in High Throughput Sequencing Output

Quantifies and removes technical noise from high-throughput sequencing data. Two approaches are used, one based on the count matrix, and one using the alignment BAM files directly. Contains several options for every step of the process, as well as tools to quality check and assess the stability of output.

Authors:Ilias Moutsopoulos [aut, cre], Irina Mohorianu [aut, ctb], Hajk-Georg Drost [ctb], Elze Lauzikaite [ctb]

noisyr_1.1.0.tar.gz
noisyr_1.1.0.zip(r-4.7-any)noisyr_1.1.0.zip(r-4.6-any)noisyr_1.1.0.zip(r-4.5-any)
noisyr_1.1.0.tgz(r-4.6-any)noisyr_1.1.0.tgz(r-4.5-any)
noisyr_1.1.0.tar.gz(r-4.7-any)noisyr_1.1.0.tar.gz(r-4.6-any)
noisyr_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
noisyr/json (API)

# Install 'noisyr' in R:

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

Bug tracker:https://github.com/core-bioinformatics/noisyr/issues

On CRAN:

4.74 score 10 stars 11 scripts 327 downloads 18 exports 53 dependencies

Last updated from:0c4b3b1f13. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	WARNING	140
source / vignettes	OK	277
linux-release	WARNING	151
macos-release	WARNING	170
macos-oldrel	WARNING	141
windows-devel	WARNING	100
windows-release	WARNING	102
windows-oldrel	WARNING	93
wasm-release	OK	124

Exports:calculate_expression_profile calculate_expression_similarity_counts calculate_expression_similarity_transcript calculate_first_minimum_density calculate_noise_threshold calculate_noise_threshold_method_statistics cast_gtf_to_genes cast_matrix_to_numeric filter_genes_transcript get_methods_calculate_noise_threshold get_methods_correlation_distance noisyr noisyr_counts noisyr_transcript optimise_window_length plot_expression_similarity remove_noise_from_bams remove_noise_from_matrix

Dependencies:BH BiocGenerics BiocParallel Biostrings bitops cli codetools cpp11 crayon doParallel dplyr farver foreach formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gtable IRanges isoband iterators KernSmooth labeling lambda.r lifecycle magrittr philentropy pillar pkgconfig poorman preprocessCore R6 RColorBrewer Rcpp RcppParallel Rhtslib rlang Rsamtools S4Vectors S7 scales Seqinfo snow tibble tidyselect utf8 vctrs viridisLite withr XVector

noisyR count matrix approach workflow

Rendered fromvignette_noisyr_counts.Rmdusingknitr::rmarkdown

Last update: 2021-06-02
Started: 2021-03-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate the expression profile of a gene	calculate_expression_profile
Calcualate the expression levels and expression levels similarity matrices using the count matrix	calculate_expression_similarity_counts
Calcualte the distance matrices using the BAM files	calculate_expression_similarity_transcript
Function to find the first local minimum of the density of a vector	calculate_first_minimum_density
Function to calculate the noise threshold for a given expression matrix and parameters	calculate_noise_threshold
Function to tabulate statistics for different methods of calculating the noise threshold	calculate_noise_threshold_method_statistics
Function to extract exon names and positions from a gtf file	cast_gtf_to_genes
Cast a matrix of any type to numeric	cast_matrix_to_numeric
Function to filter the gene table for the transcript approach	filter_genes_transcript
Show the methods for calculating a noise threshold	get_methods_calculate_noise_threshold
Show the methods for calculating correlation or distance	get_methods_correlation_distance
Run the noisyR pipeline	noisyr
Run the noisyR pipeline for the count matrix approach	noisyr_counts
Run the noisyR pipeline for the transcript approach	noisyr_transcript
Optimise the elements per window for the count matrix approach	optimise_window_length
Plot the similarity against expression levels	plot_expression_similarity
Function to remove the noisy reads from the BAM files	remove_noise_from_bams
Function to remove the noisy reads from the expression matrix	remove_noise_from_matrix