Package: DominoEffect 1.27.0

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_1.27.0.tar.gz
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DominoEffect.pdf |DominoEffect.html✨
DominoEffect/json (API)
NEWS

# 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-1.27.0(bioc 3.21)DominoEffect-1.26.0(bioc 3.20)

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

3.48 score 1 scripts 194 downloads 1 mentions 7 exports 96 dependencies

Last updated 2 months agofrom:deeeeaceec. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:align_to_unip calculate_boundary DominoEffect GPo_of_hotspots identify_hotspots import_txdb map_to_func_elem

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

Vignette for DominoEffect package

Marija Buljan and Peter Blattmann

Rendered fromVignette.Rmdusingknitr::rmarkdownon Nov 29 2024.

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