mtanic

labs

Rmd source files for the HarvardX series PH525x

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

ComplexHeatmap

Make Complex Heatmaps

bedtools2

bedtools - the swiss army knife for genome arithmetic

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

book

DNA-seq-analysis

DNA sequencing analysis notes from Ming Tang

MONOD2

MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data

umitools

Tools to handle reads sequenced with unique molecular identifiers (UMIs).

ph525x

ph525x. functions only, no data

EBI_cancer_workshop_CNV

hands-on for NGS/SNParray CNV call trainning

EBI_cancer_workshop_SNV

preinvasive

Molecular analysis of pre-invasive lung cancer samples

ezASCAT

Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R

Strategies_for_analyzing_BS-seq

Umi-Grinder

The use of UMIs for sequencing becomes more and more frequently used so we need to take them into consideration when deduplicating data aligning to the same positions

Bismark-ENCODE-WGBS

DNANexus Whole Genome Bisulphite Analysis Pipeline

methylseqplatformcomparison

scripts to analyze and generate the figures for the methyl-seq platform comparison article

ChAMP-Scripts

Some extra scripts might be used during ChAMP DNA methylation analysis