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Projects in Awesome Lists by dnbaker

A curated list of projects in awesome lists by dnbaker .

https://github.com/dnbaker/dashing

Fast and accurate genomic distances using HyperLogLog

hyperloglog indexing metagenomics sketch-data-structures

Last synced: 12 Jan 2025

https://github.com/dnbaker/sketch

C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings

bloom-filter count-min-sketch hll hyperloglog minhash sketch-data-structures

Last synced: 19 Jan 2025

https://github.com/dnbaker/bonsai

Bonsai: Fast, flexible taxonomic analysis and classification

bioinformatics database metagenomics

Last synced: 12 Jan 2025

https://github.com/dnbaker/dashing2

Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.

Last synced: 12 Jan 2025

https://github.com/dnbaker/minicore

Fast and memory-efficient clustering + coreset construction, including fast distance kernels for Bregman and f-divergences.

approximation-algorithms bregman-divergence clustering coreset importance-sampling kmeansplusplus localsearchplusplus mbkmeans

Last synced: 12 Jan 2025

https://github.com/dnbaker/bioseq

Tokenizers and Machine Learning Models for biological sequence data

biological-sequences machine-learning tokenization transformers

Last synced: 12 Jan 2025

https://github.com/dnbaker/vec

Type-generic SIMD library for optimized generic code generation

Last synced: 12 Jan 2025

https://github.com/dnbaker/aesctr

C++ implementation of AES-CTR PRNG using SIMD, based on Samuel Neves' Implementation

Last synced: 12 Jan 2025

https://github.com/dnbaker/wmh

Weighted Minhash Code

Last synced: 12 Jan 2025

https://github.com/dnbaker/mcl

Markov Clustering

Last synced: 12 Jan 2025

https://github.com/dnbaker/fastiota

Fast std::iota for contiguous memory using SIMD operations

Last synced: 12 Jan 2025

https://github.com/dnbaker/stochasticsvm

SVM trained by the PEGASOS Stochastic Subgradient Descent algorithm

classification kernel-methods pegasos svm

Last synced: 12 Jan 2025

https://github.com/dnbaker/libsimdsampling

Data- and processor- parallelism for fast weighted sampling

d2-sampling kmeanspp reservoir-sampling sampling simd

Last synced: 12 Jan 2025

https://github.com/dnbaker/10xdash

Pairwise similarity metrics for 10x barcoded RNASeq datasets

Last synced: 12 Jan 2025

https://github.com/dnbaker/khset

Simple wrappers around khset/map

Last synced: 12 Jan 2025

https://github.com/dnbaker/valptr

Stores a pointer and a value using unused bits in the pointer

Last synced: 12 Jan 2025

https://github.com/dnbaker/libkl

Kernels for fast vectorized KL divergence + related

Last synced: 12 Jan 2025

https://github.com/dnbaker/fftwrapper

RAII-based C++ wrapper of FFTW

fft fftw

Last synced: 12 Jan 2025

https://github.com/dnbaker/fpwrap

Wrap zstd/gzip/std::FILE * generically in one class template.

Last synced: 12 Jan 2025

https://github.com/dnbaker/libtorch-kseq-demo

Demo using libtorch and one-hot encoding for fastx files

Last synced: 12 Jan 2025

https://github.com/dnbaker/gds

Graph Data Structures: Generic, Space-efficient Graph Algorithms

union-find

Last synced: 12 Jan 2025

https://github.com/dnbaker/kspp

C++/RAII port of kstring_t from klib

Last synced: 12 Jan 2025

https://github.com/dnbaker/dci

Dynamic Continuous Indexing

dci indexing lsh pdci

Last synced: 12 Jan 2025

https://github.com/dnbaker/circularqueue

Circular Queue for minimizing memory allocations in deque applications

Last synced: 12 Jan 2025

https://github.com/dnbaker/simpleutilities

Miscellaneous utilities: zhead, reverse-complement, tab6

Last synced: 12 Jan 2025

https://github.com/dnbaker/distance

Distance and Meaning

Last synced: 12 Jan 2025

https://github.com/dnbaker/sv

Sparse Vector Implementation

Last synced: 12 Jan 2025

https://github.com/dnbaker/lazy

Lazy container for reduced memory footprint and optional initialization

Last synced: 12 Jan 2025

https://github.com/dnbaker/diskmat

mmap-backed blaze matrices

Last synced: 12 Jan 2025

https://github.com/dnbaker/minicore-experiments

Experiments for minicore: fast scRNA-seq clustering with various distances

Last synced: 12 Jan 2025

https://github.com/dnbaker/tilt

Biased dataloaders for PyTorch and related utilities

Last synced: 12 Jan 2025

https://github.com/dnbaker/lazy-fisher-yates

A class offering lazy iteration over a shuffled sequence.

Last synced: 12 Jan 2025

https://github.com/dnbaker/mdn

Mixture Density Networks in pytorch

Last synced: 12 Jan 2025

https://github.com/dnbaker/dashing2-binaries

Binaries for releases for Dashing2

Last synced: 12 Jan 2025

https://github.com/dnbaker/distmat

2-dimensional distance matrix for holding distances of arbitrary types.

Last synced: 12 Jan 2025

https://github.com/dnbaker/dbt

Last synced: 12 Jan 2025

https://github.com/dnbaker/lineqc

Last synced: 12 Jan 2025

https://github.com/dnbaker/cybmf

Old Utilities from BMFtools development

Last synced: 12 Jan 2025

https://github.com/dnbaker/dnbaker

Last synced: 12 Jan 2025

https://github.com/dnbaker/psitools

PSI tools

Last synced: 12 Jan 2025

https://github.com/dnbaker/project_templates

Templates for C++ projects using the sketch library

Last synced: 12 Jan 2025

https://github.com/dnbaker/linear

Linear containers for accelerated small sets/counters

Last synced: 12 Jan 2025

https://github.com/dnbaker/dlib

(Old) Shared utilities between C/C++ projects for HTSlib

Last synced: 12 Jan 2025

https://github.com/dnbaker/scavenger

Rust spatial/single-cell genomics

Last synced: 12 Jan 2025

https://github.com/dnbaker/insertsize

Last synced: 12 Jan 2025

https://github.com/dnbaker/reservoir

Reservoir sampling from Data frOm Gigantic Streams

Last synced: 12 Jan 2025

https://github.com/dnbaker/timestamper

Track subprogram runtimes

Last synced: 12 Jan 2025

https://github.com/dnbaker/rfgc

Last synced: 12 Jan 2025

https://github.com/dnbaker/maskripper

Simple utility for trimming masked ends of aligned reads

Last synced: 12 Jan 2025

https://github.com/dnbaker/minilsh

Python bindings for Locality-Sensitive Hashers, built on the minicore C++ library.

jsdlsh lsh p-stable-hashing python

Last synced: 12 Jan 2025

https://github.com/dnbaker/dnlp

A hodgepodge of NLP-related code.

Last synced: 12 Jan 2025

https://github.com/dnbaker/trie

I can not win but I haz 2 ...

Last synced: 12 Jan 2025

https://github.com/dnbaker/kf

Short Kmer Frequencies in a single pass

Last synced: 12 Jan 2025

https://github.com/dnbaker/sdsl-vec-test

Benchmarking SDSL compressed integer vector access speed and compression ratio

Last synced: 12 Jan 2025

https://github.com/dnbaker/blaze-rnla

Randomized Linear Algebra for blaze-lib

count-sketch nmf numerical-linear-algebra pca rnla

Last synced: 12 Jan 2025