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machine_learning

Machine learning in R

maftools

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

mendelianrna-seq

Code associated with the RNA-seq guided diagnosis of Mendelian disease patients

mergesvcallers

heuristics to merge structural variant calls in VCF format.

mergevcf

Python package and routines for merging VCF files

metabolomicstools

metasra-pipeline

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

mhc-prg

Population Reference Graphs for the HLA and MHC.

mice8992-2016

Code used in MiCE 8992 Spring 2016

miller

Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON

mutation-signatures

Create mutation signatures from MAF's, and decompose them into Stratton signatures

mutationalpatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

na12878

Data and analysis for NA12878 genome on nanopore

ngi-rnaseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

omim

Repo for downloading and storing OMIM data

oneliners

Useful bash one-liners for bioinformatics.

openpbta-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

pandas-cookbook

Recipes for using Python's pandas library

pepdata

Python interface to immunology and bioinformatics datasets (i.e. IEDB, cancer antigens, TCGA mutant peptides)

pgkb-ngs-pipeline

PharmGKB NGS Pipeline

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

phantompeakqualtools

This package computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

pharmacogenetics

pharmcat

The Pharmacogenomic Clinical Annotation Tool - take genome data, make haplotype calls, get CPIC annotations.

pisces

Somatic variant caller for tumor-only samples

psap-pipeline

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

pvactools

pybam

Very simple, pure python, BAM file reader