karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Genomic Data Retrieval with R

Genome Interval Arithmetic in R

dcHiC: Differential compartment analysis for Hi-C datasets

De novo annotation of young retrotransposons

an R/Shiny application for interactive creation of non-circular plots of whole genomes

Matrix dissimilarity from the differences of Moments and sparsity

Extract Sequence from Genome According to Annotation File

visual analysis of your VCF files

An easy way of MLSTyping your genomes in R.

An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests

Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec

DeepGenomeScan: A Deep Learning Approach for Whole Genome Scan (WGS) and Genome-wide Association Studies (GWAS)

acorn is an R package that examines various features of de novo variants including subsetting DNVs by individual, variant type, or genomic region; calculating features including variant change counts, lengths, and presence/absence at CpG sites; and characteristics of parental age and number of DNVs.

Scripts for .bed file genomic region annotation with various tools

Interactive web app to compute and display statistics for genomes or DNA sequences of different organisms

examination of genome size across all kingdoms

Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.

El genoma pequeño - analysis workflow for "the little genome"

R package for easy mm9 <-> mm10 / hg19 <-> hg38