mmesbahu Goto Github PK

islr-python

An Introduction to Statistical Learning (James, Witten, Hastie, Tibshirani, 2013): Python code

keras

Deep Learning for humans

krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

labs

Scripts for PH525x: Data Analysis for Genomics

lapack

LAPACK development repository

ldpred

ldsc

LD Score Regression (LDSC)

learning_random_forest

Notes and code for learning Random Forests

linsight

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

m3vcftools

matahari

🔎 I Spy With My Little Eye

metasv

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing

minimac3

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

minimac4

ml

mmesbahu.github.io

Personal Page

modernizing-undergrad-stat-curric

JSM 2017 session on Modernizing the Undergraduate Statistics Curriculum

mpitutorial

MPI programming lessons in C and executable code examples

multibugs

Multi-core BUGS for fast Bayesian inference of large hierarchical models

multichoose

generate multiset combinations (n multichoose k)

networks_correction

Code to reproduce analysis in "Addressing confounding artifacts in reconstruction of gene co-expression networks"

neural-networks-and-deep-learning

Code samples for my book "Neural Networks and Deep Learning"

nextgenmap

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

ngs

NGS Language Bindings

ngs-tools

ngs-utils

Collection of notes and scripts related to NGS

ngspopgen

Population genetics analyses from NGS data

ngstools

Programs to analyse NGS data for population genetics purposes