Introduction | Key Features | Technical Pipeline & Parameter Configurations | Gene Mining Function Arguments | Target Reference Genome Assemblies | Step-by-Step Executions | Workflow 1: Instant Local Tracking Engine (CRAN Safe) | Workflow 2: Online Real-Time Web Scraping Mode | Workflow 3: Custom Haplotype Range Testing (geneSNPcustom) | Genomic Data Summarization & Visualization | Parsing and Summarizing Genotypic Data | Mapping Chromosomal Density Charts (plot_SNP) | Visualizing Frequency Histograms (plot_summariseSNP) | System Output Layout | Support & Package Maintenance | Glossary
Package: geneNR 3.0.0
geneNR: Automated Gene Identification for Post-GWAS and QTL Analysis
Facilitates the post-Genome Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) analysis of identifying candidate genes within user-defined search window, based on the identified Single Nucleotide Polymorphisms (SNPs) as given by Mazumder AK (2024) <doi:10.1038/s41598-024-66903-3>. It supports candidate gene analysis for wheat and rice. Just import your GWAS result as explained in the sample_data file and the function does all the manual search and retrieve candidate genes for you, while exporting the results into ready-to-use output.
Authors:
geneNR_3.0.0.tar.gz
geneNR_3.0.0.zip(r-4.7)geneNR_3.0.0.zip(r-4.6)geneNR_3.0.0.zip(r-4.5)
geneNR_3.0.0.tgz(r-4.6-any)geneNR_3.0.0.tgz(r-4.5-any)
geneNR_3.0.0.tar.gz(r-4.7-any)geneNR_3.0.0.tar.gz(r-4.6-any)
geneNR_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geneNR/json (API)
| # Install 'geneNR' in R: |
| install.packages('geneNR', repos = c('https://nirmalaruban.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- sample_data_rice - Sample Data
- sample_data_rice_qtl - Sample Data
- sample_data_wheat - Sample Data
- sample_data_wheat_custom - Sample Data
- sample_data_wheat_qtl - Sample Data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:b34c8c709b. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 171 | ||
| source / vignettes | OK | 230 | ||
| linux-release-x86_64 | OK | 168 | ||
| macos-release-arm64 | OK | 87 | ||
| macos-oldrel-arm64 | OK | 86 | ||
| windows-devel | OK | 81 | ||
| windows-release | OK | 89 | ||
| windows-oldrel | OK | 93 | ||
| wasm-release | OK | 168 |
Exports:geneQTLgeneSNPgeneSNPcustomimport_hmpimport_vcfplot_SNPplot_summariseSNPsummariseSNPsummariseSNP_vcf
Dependencies:apeaskpassbitbit64clicliprclustercpp11crayoncurldigestdplyrfarvergenericsggplot2ggrepelgluegtablehmshttrisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemusemgcvmimenlmeopensslpermutepillarpinfsc50pkgconfigprettyunitsprogressR6RColorBrewerRcppreadrrlangrvestS7scalesselectrstringistringrsystibbletidyselecttzdbutf8vcfRvctrsveganviridisLitevroomwithrwritexlxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identifies Candidate Genes based on identified Quantitative Trait Loci (QTL) analysis | geneQTL |
| Identifies Candidate Genes based on identified Single Nucleotide Polymorphisms (SNPs) from Genome Wide Association Studies (GWAS) Analysis | geneSNP |
| Identifies Candidate Genes based on identified Single Nucleotide Polymorphisms (SNPs) from Genome Wide Association Studies (GWAS) Analysis | geneSNPcustom |
| Imports Hapmap genotypic data file | import_hmp |
| Imports VCF (Variant Call Format) data file | import_vcf |
| Plot SNP Distribution on Chromosome Map | plot_SNP |
| Plot SNP Distribution Across Chromosomes | plot_summariseSNP |
| Sample Data | sample_data_rice |
| Sample Data | sample_data_rice_qtl |
| Sample Data | sample_data_wheat |
| Sample Data | sample_data_wheat_custom |
| Sample Data | sample_data_wheat_qtl |
| Distribution of SNPs Across Chromosomes | summariseSNP |
| Distribution of SNPs Across Chromosomes from VCF | summariseSNP_vcf |
