Package: cageminer 1.13.0

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]

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NEWS

# 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-1.13.0(bioc 3.21)cageminer-1.12.0(bioc 3.20)

software snp functionalprediction genomewideassociation geneexpression networkenrichment variantannotation functionalgenomics network

4.30 score 1 stars 2 scripts 139 downloads 8 exports 198 dependencies

Last updated 2 months agofrom:ce80090a70. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	OK	Dec 19 2024
R-4.5-linux	OK	Dec 19 2024
R-4.4-win	OK	Dec 19 2024
R-4.4-mac	OK	Dec 19 2024
R-4.3-win	OK	Dec 19 2024
R-4.3-mac	OK	Dec 19 2024

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 BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt BioNERO Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate circlize cli clue cluster coda codetools colorspace commonmark ComplexHeatmap cpp11 crayon curl data.table DBI dbplyr DelayedArray dichromat digest doParallel dplyr dynamicTreeCut edgeR ensembldb evaluate fansi farver fastcluster fastmap filelock fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GENIE3 GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong GGally ggbio ggdendro ggnetwork ggplot2 ggrepel ggstats ggtext GlobalOptions glue GO.db graph gridExtra gridtext gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph impute infotheo intergraph IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minet munsell NetRep network nlme nnet openssl OrganismDbi patchwork pillar pkgconfig plogr plyr png preprocessCore prettyunits progress ProtGenerics purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RCurl reshape2 restfulr RhpcBLASctl Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shape sna snow SparseArray statmod statnet.common stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite WGCNA withr xfun XML xml2 xtable XVector yaml zlibbioc

Mining high-confidence candidate genes with cageminer

Fabricio Almeida-Silva, Thiago Motta Venancio

Rendered fromcageminer.Rmdusingknitr::rmarkdownon Dec 19 2024.

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