Daniel-Liu-c0deb0t/UMICollapse

Stars
58
Rank 516,103 (Top 11 %)
Language
Java
License
MIT License
Created almost 6 years ago
Updated 8 months ago

Daniel-Liu-c0deb0t/UMICollapse

Daniel-Liu-c0deb0t

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Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

uwu

fastest text uwuifier in the west

Java-Machine-Learning

Deep learning library for Java, with fully connected, convolutional, and recurrent layers. Also features many gradient descent optimization algorithms.

block-aligner

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

Jupyter Notebook

cute-nucleotides

Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.

triple_accel

Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance calculations and string search.

Adversarial-point-perturbations-on-3D-objects

New distributional and shape attacks on neural networks that process 3D point cloud data.

3D-Neural-Network-Adversarial-Attacks

Research on adversarial attacks and defenses for deep neural network 3D point cloud classifiers like PointNet and PointNet++.

ANTISEQUENCE

Rust library for processing sequencing reads.

simple-saca

Hardware go brrr bounded context suffix array construction algorithm

dlb-kmer-sampling

Optimal distance lower bound k-mer sampling.

9S

Basic Rust program that uses multiple threads to send and receive pings.

spliced-aligner

Spliced aligner.

Java-Fuzzy-Search

A general, multi-threaded fuzzy searching language, called fuzzysplit, that is built on top of a fast and flexible Java fuzzy search library. Can be applied to demultiplex and trim DNA.

diff-align

Differentiable position-specific probability matrix alignment.

General-Algorithms

A variety of algorithm implementations and short classes, mostly for competitive programming and machine learning.

replit_audio

Rust library for playing audio in repl.it.

WWDC-2020-Coronavirus-Comparison

Efficiently comparing the 2019 coronavirus genome with a couple of other coronaviruses in Swift.

rust-cloc

Count lines from files in a directory.

frfr

Parallelized Ukkonen/Myer's edit distance algorithm, fr fr.

diff-bench-paper

Edits to the supplementary data of the difference recurrence alignment paper.

simulate-seqs

Simulate sequences.

reCall

Interpreter for reCall, a dynamically typed scripting language that emphasizes recursion. Also contains object-oriented and functional features.

Maze-Solver

2D grid-based maze solver that is written in Java. Uses Swing for GUI and contains 8 different methods for solving mazes.