Daniel-Liu-c0deb0t

cs boi @ucla | prev genomics/rust/ml @google, @10XGenomics | uwu

Pinned Repositories

3D-Neural-Network-Adversarial-Attacks
Research on adversarial attacks and defenses for deep neural network 3D point cloud classifiers like PointNet and PointNet++.
Language:Python23 5 58
Adversarial-point-perturbations-on-3D-objects
New distributional and shape attacks on neural networks that process 3D point cloud data.
Language:Python37 4 37
ANTISEQUENCE
Rust library for processing sequencing reads.
Language:Rust21 4 43
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.
Language:Jupyter Notebook124 7 207
cute-nucleotides
Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.
Language:Rust116 6 14
Java-Machine-Learning
Deep learning library for Java, with fully connected, convolutional, and recurrent layers. Also features many gradient descent optimization algorithms.
Language:Java134 15 425
triple_accel
Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance calculations and string search.
Language:Rust103 6 1212
UMICollapse
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.
Language:Java63 3 318
uwu
fastest text uwuifier in the west
Language:Rust1.4k 14 2441
best
Bam Error Stats Tool (best): analysis of error types in aligned reads.
Language:Rust124 9 97

Daniel-Liu-c0deb0t's Repositories

Daniel-Liu-c0deb0t/uwu
fastest text uwuifier in the west
Language:Rust1.4k 14 2441
Daniel-Liu-c0deb0t/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.
Language:Jupyter Notebook124 7 207
Daniel-Liu-c0deb0t/triple_accel
Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance calculations and string search.
Language:Rust103 6 1212
Daniel-Liu-c0deb0t/UMICollapse
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.
Language:Java63 3 318
Daniel-Liu-c0deb0t/Adversarial-point-perturbations-on-3D-objects
New distributional and shape attacks on neural networks that process 3D point cloud data.
Language:Python37 4 37
Daniel-Liu-c0deb0t/ANTISEQUENCE
Rust library for processing sequencing reads.
Language:Rust21 4 43
Daniel-Liu-c0deb0t/simple-saca
Hardware go brrr bounded context suffix array construction algorithm
Language:Rust17 4 43
Daniel-Liu-c0deb0t/dlb-kmer-sampling
Optimal distance lower bound k-mer sampling.
Language:Rust12
Daniel-Liu-c0deb0t/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.
Language:Java5 3 21
Daniel-Liu-c0deb0t/diff-align
Differentiable position-specific probability matrix alignment.
Language:Python4 2 0
Daniel-Liu-c0deb0t/frfr
Parallelized Ukkonen/Myer's edit distance algorithm, fr fr.
Language:Rust2 1 0
Daniel-Liu-c0deb0t/libsais-rs
rust bindings to libsais
Language:Rust2 2 0
Daniel-Liu-c0deb0t/rust-cloc
Count lines from files in a directory.
Language:Rust2 2 0
Daniel-Liu-c0deb0t/consulting
Consulting website.
Language:JavaScript1 1 0
Daniel-Liu-c0deb0t/diff-bench-paper
Edits to the supplementary data of the difference recurrence alignment paper.
Language:C++1 4 0
Daniel-Liu-c0deb0t/simulate-seqs
Simulate sequences.
Language:Rust1 2 0
Daniel-Liu-c0deb0t/adaptivebandbench
Benchmark on adaptive banded algorithm
Language:C2 0
Daniel-Liu-c0deb0t/best
Bam Error Stats Tool (best): analysis of error types in aligned reads.
Language:Rust1 0
Daniel-Liu-c0deb0t/Blog
My blog.
Language:SCSS2 0
Daniel-Liu-c0deb0t/Daniel-Liu-c0deb0t.github.io
My personal website.
Language:HTML3 0
Daniel-Liu-c0deb0t/dotfiles
Linux dot files.
Language:Shell3 0
Daniel-Liu-c0deb0t/edlib-rs
rust binding to edlib
Language:C++1 01
Daniel-Liu-c0deb0t/FLAMAnalysis
Data Analysis For FLAM-Seq Third Generation RNA Sequencing
Language:Python2 0
Daniel-Liu-c0deb0t/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
Language:C1 0
Daniel-Liu-c0deb0t/parasailors-new
Rust bindings to parasail, a SIMD-accelerated pairwise sequence alignment library.
Language:Rust1 0
Daniel-Liu-c0deb0t/rust-alignbench
Pairwise nucleotide alignment benchmark of Rust bindings
Language:Jupyter Notebook1 0
Daniel-Liu-c0deb0t/rust-bio
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
Language:Rust2 0
Daniel-Liu-c0deb0t/rust-bk-tree
A BK-tree implementation in Rust.
Language:Rust1 0
Daniel-Liu-c0deb0t/rust-wfa2
Rust binding for WFA2-lib
Language:Rust1 01
Daniel-Liu-c0deb0t/seq_io
FASTA and FASTQ parsing in Rust
Language:Rust1 0