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Schaudge's Projects

megalodon icon megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

metabuli icon metabuli

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

metacache icon metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

metagraph icon metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

metaphlan icon metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

metheor icon metheor

:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments

minigraph icon minigraph

Proof-of-concept seq-to-graph mapper and graph generator

minijinja icon minijinja

MiniJinja is a powerful but minimal dependency template engine for Rust

minimap2 icon minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mistral-src icon mistral-src

Reference implementation of Mistral AI 7B v0.1 model.

mitie icon mitie

MITIE: library and tools for information extraction

mlpack icon mlpack

mlpack: a scalable C++ machine learning library

mlxtend icon mlxtend

A library of extension and helper modules for Python's data analysis and machine learning libraries.

mmseqs2 icon mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

models icon models

Models and examples built with TensorFlow

modern-cpp-tutorial icon modern-cpp-tutorial

📚 Modern C++ Tutorial: C++11/14/17/20 On the Fly | https://changkun.de/modern-cpp/

moni icon moni

MONI: A Pangenomic Index for Finding MEMs

monocle3 icon monocle3

an analysis toolkit for single-cell RNA-Seq experiments

mosdepth icon mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

mothur icon mothur

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

msnap icon msnap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

multiqc icon multiqc

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

muscle icon muscle

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

music icon music

Multi-subject Single Cell Deconvolution

nccl icon nccl

Optimized primitives for collective multi-GPU communication

ndarray icon ndarray

ndarray: an N-dimensional array with array views, multidimensional slicing, and efficient operations

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