Package: DominoEffect 1.33.0

Marija Buljan

DominoEffect: Identification and Annotation of Protein Hotspot Residues

The functions support identification and annotation of hotspot residues in proteins. These are individual amino acids that accumulate mutations at a much higher rate than their surrounding regions.

Authors:Marija Buljan and Peter Blattmann

DominoEffect_1.33.0.tar.gz
DominoEffect_1.33.0.zip(r-4.7)DominoEffect_1.33.0.zip(r-4.6)DominoEffect_1.33.0.zip(r-4.5)
DominoEffect_1.33.0.tgz(r-4.6-any)DominoEffect_1.33.0.tgz(r-4.5-any)
DominoEffect_1.33.0.tar.gz(r-4.7-any)DominoEffect_1.33.0.tar.gz(r-4.6-any)
DominoEffect_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DominoEffect/json (API)

# Install 'DominoEffect' in R:

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

Datasets:

DominoData - Sample data
SnpData - Sample data
TestData - Sample data

On BioConductor:DominoEffect-1.33.0(bioc 3.24)DominoEffect-1.32.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software somaticmutation proteomics sequencematching alignment

3.70 score 1 scripts 1 mentions 7 exports 92 dependencies

Last updated from:cb54b0bac0. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	206
linux-devel-x86_64	NOTE	576
source / vignettes	OK	328
linux-release-x86_64	NOTE	535
macos-release-arm64	NOTE	381
macos-oldrel-arm64	NOTE	326
windows-devel	NOTE	415
windows-release	NOTE	369
windows-oldrel	NOTE	415
wasm-release	OK	166

Exports:align_to_unip calculate_boundary DominoEffect GPo_of_hotspots identify_hotspots import_txdb map_to_func_elem

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr fastmap filelock formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr pwalign R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 VariantAnnotation vctrs withr XML xml2 XVector yaml

Vignette for DominoEffect package

Rendered fromVignette.Rmdusingknitr::rmarkdown

Last update: 2021-04-16
Started: 2018-02-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Align protein segnent around the hotspot to the UniProt/Swiss-Prot KB sequence.	align_to_unip
calculate_boundary	calculate_boundary
Sample data	DominoData SnpData TestData
Identification of significant mutation hotspot residues.	DominoEffect
Converts hotspot mutation table into a GPo object	GPo_of_hotspots
Identify hotspots	identify_hotspots
Imports txdb data and converts it into format required for DominoEffect package	import_txdb
Functional annotation of significant hotspot residues.	map_to_func_elem