macs

MACS -- Model-based Analysis of ChIP-Seq

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

manta

Structural variant and indel caller for mapped sequencing data

mapmuts

Map mutations and infer amino-acid preferences from overlapping paired-end amino acid reads

metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

mg14

mg14's favourite R functions

migec

A RepSeq processing swiss-knife

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

momocs

Morphometrics using R

monusac-isbi-2020

[TMI'2021][ISBI MoNuSAC'2020] 11th place solution to Multi-organ nuclei segmentation and classification challenge.

mosclip

Multi Omics Survival Clip

msisensor

microsatellite instability detection using paired tumor-normal

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

mutationalpatterns

R package for extracting and visualizing mutational patterns in SNV data

mutationalprofiles

netuser15

igraph tutorial at the userR 2015 conference

networkanalysistalk_april2015

talk and code for 17 April 2015 'Meet the Geek' seminar series

networkd3

D3 JavaScript Network Graphs from R

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

nozzle

Nozzle is a report generation toolkit for data analysis pipelines implemented in R.

optitype

Precision HLA typing from next-generation sequencing data

paperrmdtemplate

Here is a template to use for basic academic reports

pathml

Tools for computational pathology

pathomicfusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

phyc

Clustering cancer evolutionary trees

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

pipelines_for_chip-seq_analysis

Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.

plot_chippeaks

pvac-seq

A cancer immunotherapy pipeline

pyradiomics

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks.