Package: umiAnalyzer 1.0.0

Stefan Filges

umiAnalyzer: Tools for Analyzing Sequencing Data with Unique Molecular Identifiers

Tools for analyzing sequencing data containing unique molecular identifiers generated by 'UMIErrorCorrect' (<https://github.com/stahlberggroup/umierrorcorrect>).

Authors:Stefan Filges [aut, cre], Gustav Johansson [ctb]

umiAnalyzer_1.0.0.tar.gz
umiAnalyzer_1.0.0.zip(r-4.5)umiAnalyzer_1.0.0.zip(r-4.4)umiAnalyzer_1.0.0.zip(r-4.3)
umiAnalyzer_1.0.0.tgz(r-4.4-any)umiAnalyzer_1.0.0.tgz(r-4.3-any)
umiAnalyzer_1.0.0.tar.gz(r-4.5-noble)umiAnalyzer_1.0.0.tar.gz(r-4.4-noble)
umiAnalyzer_1.0.0.tgz(r-4.4-emscripten)umiAnalyzer_1.0.0.tgz(r-4.3-emscripten)
umiAnalyzer.pdf |umiAnalyzer.html✨
umiAnalyzer/json (API)
NEWS

# Install 'umiAnalyzer' in R:

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

Bug tracker:https://github.com/sfilges/umianalyzer/issues

On CRAN:

targeted-sequencing unique-molecular-identifiers variant-analysis

4.46 score 58 scripts 127 downloads 27 exports 115 dependencies

Last updated 3 years agofrom:e1d7bb20cf. Checks:OK: 6 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 13 2024
R-4.5-win	OK	Nov 13 2024
R-4.5-linux	WARNING	Nov 13 2024
R-4.4-win	OK	Nov 13 2024
R-4.4-mac	OK	Nov 13 2024
R-4.3-win	OK	Nov 13 2024
R-4.3-mac	OK	Sep 30 2024

Exports:addMetaData addUmiSample AmpliconHeatmap AmpliconPlot BarcodeFamilyHistogram beta_binom callVariants createUmiExperiment createUMIexperiment_Debarcer createUmiSample createUMIsample_Debarcer download_template filterUmiObject filterVariants findConsensusReads generateVCF getFilteredData getMetaData importBedFile importDesign mergeAssays parseBamFiles QCplot runUmiVisualizer saveConsData timeSeriesGrid UmiCountsPlot

Dependencies:askpass base64enc BH BiocGenerics BiocManager BiocParallel Biostrings bit bit64 bitops bslib cachem cli clipr codetools colorspace commonmark cpp11 crayon crosstalk curl data.table digest dplyr DT evaluate fansi farver fastmap fontawesome forcats formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable highr hms htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pheatmap pillar pkgconfig plotly prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr Rhtslib rlang rmarkdown Rsamtools S4Vectors sass scales shiny shinydashboard shinyFiles shinyWidgets snow sourcetools stringi stringr sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom withr xfun xtable XVector yaml zlibbioc

umiAnalyzer vignette

Stefan Filges

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2021-11-25
Started: 2021-11-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add metaData	addMetaData
Add UMI sample to an existing experiment object	addUmiSample
Amplicon heatmap	AmpliconHeatmap
Generate Amplicon plots	AmpliconPlot
Consensus depth histograms	BarcodeFamilyHistogram
Beta binomial model	beta_binom
callVariants using beta binomial distribution	callVariants
Method for creating a UMI experiment object	createUmiExperiment
Method for creating a UMI experiment object	createUMIexperiment_Debarcer
createUmiSample	createUmiSample
Method for creating a UMIsample object	createUMIsample_Debarcer
Download meta data template	download_template
Method for filtering UMIexperiment and sample objects	filterUmiObject
Filter variants based on p values or depth	filterVariants
Find consensus reads A function to analyze consensus read tables generated with parseBamFiles or a UMIexperiment object containing reads.	findConsensusReads
Generate VCF file from UMI sample or UMI experiment object	generateVCF
Method for retrieving filtered data	getFilteredData
Retrieve meta data by name.	getMetaData
Import bed file	importBedFile
Import experimental design meta data such as replicates, treatments, categorical variables.	importDesign
Merge assays	mergeAssays
Function to parse bam files	parseBamFiles
Generate QC plots	QCplot
Function to run the umiVisualizer shiny app	runUmiVisualizer
Save consensus data	saveConsData
UMIexperiment data generated with SiMSen-Seq	simsen
Plot time series data	timeSeriesGrid
Plot UMI counts	UmiCountsPlot
UMIexperiment class	UMIexperiment UMIexperiment-class
UMIsample class	UMIsample UMIsample-class