Package: cageminer 1.19.0

Fabrício Almeida-Silva

cageminer: Candidate Gene Miner

This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.

Authors:Fabrício Almeida-Silva [aut, cre], Thiago Venancio [aut]

cageminer_1.19.0.tar.gz
cageminer_1.19.0.zip(r-4.7)cageminer_1.19.0.zip(r-4.6)cageminer_1.19.0.zip(r-4.5)
cageminer_1.19.0.tgz(r-4.6-any)cageminer_1.19.0.tgz(r-4.5-any)
cageminer_1.19.0.tar.gz(r-4.7-any)cageminer_1.19.0.tar.gz(r-4.6-any)
cageminer_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cageminer/json (API)

# Install 'cageminer' in R:

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

Bug tracker:https://github.com/almeidasilvaf/cageminer/issues

Datasets:

chr_length - Pepper chromosome lengths
gcn - Simulation of the output list from BioNERO::exp2gcn() with pepper data
gene_ranges - Genomic coordinates of pepper genes
guides - Guide genes associated with defense and resistance to oomycetes
hubs - Example hub genes for the network stored in the gcn object
mine2 - Example output from mine_step2
mined_candidates - Example output from mined_candidates
pepper_se - Gene expression data from Kim et al., 2018.
snp_pos - Capsicum annuum SNPs associated with resistance to Phytophthora root rot.
tfs - Pepper transcription factors

On BioConductor:cageminer-1.19.0(bioc 3.24)cageminer-1.18.0(bioc 3.23)

software snp functionalprediction genomewideassociation geneexpression networkenrichment variantannotation functionalgenomics network

4.48 score 1 stars 10 scripts 8 exports 182 dependencies

Last updated from:2cc1c547e1. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	263
linux-devel-x86_64	OK	523
source / vignettes	OK	416
linux-release-x86_64	OK	543
macos-release-arm64	OK	483
macos-oldrel-arm64	OK	323
windows-devel	OK	419
windows-release	OK	434
windows-oldrel	OK	409
wasm-release	OK	267

Exports:mine_candidates mine_step1 mine_step2 mine_step3 plot_snp_circos plot_snp_distribution score_genes simulate_windows

Dependencies:abind annotate AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel BioNERO Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo circlize cli clue cluster coda codetools colorspace commonmark ComplexHeatmap cpp11 crayon curl data.table DBI DelayedArray dichromat digest doParallel dplyr dynamicTreeCut edgeR ensembldb evaluate farver fastcluster fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GENIE3 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggbio ggdendro ggnetwork ggplot2 ggrepel ggtext GlobalOptions glue graph gridExtra gridtext gtable highr Hmisc htmlTable htmltools htmlwidgets httr igraph impute infotheo intergraph IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle limma litedown locfit magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minet NetRep network nlme nnet openssl OrganismDbi patchwork pillar pkgconfig plyr png preprocessCore ProtGenerics R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RCurl reshape2 restfulr RhpcBLASctl Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo shape sna snow SparseArray statmod statnet.common stringi stringr SummarizedExperiment survival sva sys tibble tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite WGCNA withr xfun XML xml2 xtable XVector yaml

Mining high-confidence candidate genes with cageminer

Rendered fromcageminer.Rmdusingknitr::rmarkdown

Last update: 2022-09-21
Started: 2021-03-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Pepper chromosome lengths	chr_length
Simulation of the output list from BioNERO::exp2gcn() with pepper data	gcn
Genomic coordinates of pepper genes	gene_ranges
Guide genes associated with defense and resistance to oomycetes	guides
Example hub genes for the network stored in the gcn object	hubs
Mine high-confidence candidate genes in a single step	mine_candidates
Step 1: Get all putative candidate genes for a given sliding window	mine_step1
Step 2: Get candidates in modules enriched in guide genes	mine_step2
Step 3: Select candidates based on gene significance	mine_step3
Example output from mine_step2()	mine2
Example output from mined_candidates()	mined_candidates
Gene expression data from Kim et al., 2018.	pepper_se
Circos plot of SNP distribution across chromosomes	plot_snp_circos
Plot a barplot of SNP distribution across chromosomes	plot_snp_distribution
Score candidate genes and select the top n genes	score_genes
Simulate number of genes for each sliding window	simulate_windows
Capsicum annuum SNPs associated with resistance to Phytophthora root rot.	snp_pos
Pepper transcription factors	tfs