tmap

IGV (Integrative Genomics Viewer) — high-performance Java desktop application for interactive visualization and exploration of genomic data. Supports BAM/CRAM alignments, VCF variants, BED/GFF annotat

2 shared topics • 2 shared operations

Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH

2 shared topics • 1 shared operation

dmrseq is an R/Bioconductor package for detecting differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS) data. It fits a generalized least squares model with a smooth c

2 shared topics • 1 shared operation

NgsRelate — pairwise relatedness estimation from NGS data using genotype likelihoods. Estimates kinship coefficients, R0/R1/KING-robust statistics, and inbreeding coefficients from VCF/BCF files or AN

2 shared topics • 1 shared operation

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

2 shared topics • 1 shared operation