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bamtofreq

Converts mapped next-generation sequencing reads in BAM format to the tabular frequency file format that is used by geno2pheno[ngs-freq]

bioconda-recipes

Conda recipes for the bioconda channel.

deeptime

Deep learning meets molecular dynamics.

deeptime-vampnet-tensorflow-gpu-install

install the deeptime package vampnet (including nvidia drivers + tensorflow gpu install)

fastqtofreq

Uses MinVar and bamToFreq to transform NGS reads (FASTQ) to frequency files (CSV)

geno2phenotb

Machine learning based engine to predict Mycobacterium tuberculosis drug resistance using whole-genome sequencing data

gpcca

GPCCA: Generalized Perron Cluster Cluster Analysis program to coarse-grain reversible and non-reversible Markov State Models.

gromacs-crash-course

2 days course to learn basic Linux terminal and GOMACS usage

install-deeptime-time-lagged-autoencoder

Instructions to install the time-lagged autoencoder package from deeptime, based on pytorch.

malariavaccineefficacyprediction

msmtools

Tools for estimating and analyzing Markov state models

nestedcv

NestedCV: repeated nested stratified cross-validation

plasmofab

post-aistats2017

New experiments

print-on-nums11

how to move files to nums11 server and print them

py-project-example

This repository is an example on how to structure you python project.

pygpcca

pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state models.

python

pytorch-gpu-install

Instructions for installing pytorch to run on GPU

sampleproject

A sample project that exists for PyPUG's "Tutorial on Packaging and Distributing Projects"

shields

Concise, consistent, and legible badges in SVG and raster format

smop

Small Matlab to Python compiler

sra_read_downloader

A handy script for downloading reads from any kind of accession from the SRA.

tbdb

Standard database for the TBProfiler tool

tbprofiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

tensorflow-build

TensorFlow binaries supporting AVX, FMA, SSE

tensorflow-gpu-install-ubuntu-16.04

Tensorflow GPU install instructions for ubuntu 16.04 - Deep learning

use-remote-jupyter-notebook

How to use notebboks on your remote server in your local browser via ssh.