Package: GARCOM 1.2.2

GARCOM: Gene and Region Counting of Mutations ("GARCOM")

Gene and Region Counting of Mutations (GARCOM) package computes mutation (or alleles) counts per gene per individuals based on gene annotation or genomic base pair boundaries. It comes with features to accept data formats in plink(.raw) and VCF. It provides users flexibility to extract and filter individuals, mutations and genes of interest.

Authors:Sanjeev Sariya [aut, cre, cph], Giuseppe Tosto [aut, cph]

GARCOM_1.2.2.tar.gz
GARCOM_1.2.2.zip(r-4.5)GARCOM_1.2.2.zip(r-4.4)GARCOM_1.2.2.zip(r-4.3)
GARCOM_1.2.2.tgz(r-4.4-any)GARCOM_1.2.2.tgz(r-4.3-any)
GARCOM_1.2.2.tar.gz(r-4.5-noble)GARCOM_1.2.2.tar.gz(r-4.4-noble)
GARCOM_1.2.2.tgz(r-4.4-emscripten)GARCOM_1.2.2.tgz(r-4.3-emscripten)
GARCOM.pdf |GARCOM.html✨
GARCOM/json (API)
NEWS

# Install 'GARCOM' in R:
install.packages('GARCOM', repos = c('https://complexgenome.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/complexgenome/garcom/issues

Datasets:

On CRAN:

geneticsmutation

2.70 score 2 scripts 220 downloads 4 exports 34 dependencies

Last updated 2 years agofrom:53ad17a654. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:gene_annot_countsgene_pos_countsvcf_counts_annotvcf_counts_SNP_genecoords

Dependencies:apecliclusterdata.tabledigestdplyrfansigenericsgluelatticelifecyclemagrittrMASSMatrixmemusemgcvnlmepermutepillarpinfsc50pkgconfigR6Rcpprlangstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
gene annotation countsgene_annot_counts
gene position countsgene_pos_counts
genecoordgenecoord
recodedgenrecodedgen
sample_chr21_vcfsample_chr21_vcf
snpgenesnpgene
snppossnppos
gene annotation counts using VCF datavcf_counts_annot
VCF gene position countsvcf_counts_SNP_genecoords