Package: geneHummus 1.0.11

Jose V. Die

geneHummus: A Pipeline to Define Gene Families in Legumes and Beyond

A pipeline with high specificity and sensitivity in extracting proteins from the RefSeq database (National Center for Biotechnology Information). Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family. The pipelines implements an automatic approach for the identification of gene families based on the conserved domains that specifically define that family. See Die et al. (2018) <doi:10.1101/436659> for more information and examples.

Authors:Jose V. Die [aut, cre], Moamen M. Elmassry [ctb], Kimberly H. LeBlanc [ctb], Olaitan I. Awe [ctb], Allissa Dillman [ctb], Ben Busby [aut]

geneHummus_1.0.11.tar.gz
geneHummus_1.0.11.zip(r-4.7)geneHummus_1.0.11.zip(r-4.6)geneHummus_1.0.11.zip(r-4.5)
geneHummus_1.0.11.tgz(r-4.6-any)geneHummus_1.0.11.tgz(r-4.5-any)
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geneHummus_1.0.11.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
geneHummus/json (API)

# Install 'geneHummus' in R:

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

Bug tracker:https://github.com/ncbi-hackathons/genehummus/issues

Datasets:

legumesIds - NCBI taxonomy ids for the legume family
my_legumes - ARF proteins per legume specie

On CRAN:

4.20 score 8 stars 3 scripts 185 downloads 2 mentions 7 exports 26 dependencies

Last updated from:1fb3618176. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	136
source / vignettes	OK	205
linux-release-x86_64	WARNING	130
macos-release-arm64	WARNING	120
macos-oldrel-arm64	WARNING	138
windows-devel	WARNING	89
windows-release	WARNING	88
windows-oldrel	WARNING	90
wasm-release	OK	115

Exports:accessions_by_spp accessions_from_spp filterArch_ids getAccessions getArch_ids getArch_labels getProteins_from_tax_ids

Dependencies:askpass cli curl dplyr generics glue httr jsonlite lifecycle magrittr mime openssl pillar pkgconfig R6 rentrez rlang stringi stringr sys tibble tidyselect utf8 vctrs withr XML

Help page	Topics
Compute the total number of accession proteins per species	accessions_by_spp
Extract the accession ids (XP accession) for a given organism	accessions_from_spp
Get acessions and organism for each protein identifier	accessions_warning
Get architecture identifiers for the conserved domains	archids_warning
Get the protein identifiers	extract_proteins
Filter the protein architectures based on conserved domains	filterArch_ids
Filter protein architectures based on conserved domains	filterarchids_warning
genehummus: A pipeline to define gene families in Legumes and beyond	geneHummus-package geneHummus
Get the species name from the description sequence	get_spp
Get the acessions ids and the organism for each protein identifier	getAccessions
Get the potential architecture identifiers for the conserved domains	getArch_ids
Get the description label for a protein architecture identifier	getArch_labels
Get the RefSeq protein identifiers for the given taxonomic species	getProteins_from_tax_ids
Get the protein identifiers for a given architecture	getProtlinks
Get the electronic architecture for a conserved domain	getSparcleArchs
Get description label for a protein architecture identifier	labels_warning
NCBI taxonomy ids for the legume family	legumesIds
ARF proteins per legume specie	my_legumes
Get RefSeq protein identifiers for the given taxonomic species	proteins_warning
Build a list containing N elements per element list	sizeIds

Package: geneHummus 1.0.11

geneHummus: A Pipeline to Define Gene Families in Legumes and Beyond

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