methylKit -- DNA Methylation Analysis in R

DMRcate — R/Bioconductor package for identifying differentially methylated regions (DMRs) from Illumina Infinium arrays (450K, EPIC, EPICv2) and whole genome bisulfite sequencing (WGBS/RRBS) data. Use

3 shared topics • 1 shared operation

VSEARCH — open-source, multithreaded alternative to USEARCH for amplicon and metagenomics sequence analysis. Performs dereplication, chimera detection (de novo and reference-based), OTU/ASV clustering

2 shared topics • 2 shared operations

vt — C++ command-line variant tool set for manipulating VCF files. Provides variant normalization (left-alignment and trimming), multiallelic decomposition, VCF summary statistics (peek), annotation,

2 shared topics • 2 shared operations

Spectre is an R toolkit for high-dimensional single-cell cytometry and imaging analysis, including data import (CSV/FCS), metadata integration, arcsinh/logicle transformation, clustering (FlowSOM, Phe

1 shared topic • 3 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