mahmudhera Goto Github PK

2022-paper-protein-kmers

Forked from bluegenes

accelarated_sketch_comparison

Investigation of GPU acceleration in many-to-many sketch comparison

annotate_genomes_with_ncbi_taxid

artificial-neural-network-based-image-classifier

Implementation of a neural network from scratch by coding the backpropagation algorithm.

associative-cache

An associative L1 and L2 cache simulator

cami_ani_binning

Using ani calculated using FracMinHash, this repository will assign contigs to bins. Data collected from the CAMI website.

cf-solutions

compare-constants-in-cosine-proof

Comparing a few constants that mathematically showed up in the proof of cosine similarity

compare_fmh_simka_mash

Compare FracMinHash, SIMKA, and Mash in computing pairwise distances for a number of genomes/metagenomes etc.

compare_ground_truths

cosine-sim-fmh-simulation

Start with a long random 0-1 vector. Take random columns of that vector. See if cosine similarity using these approximate original cosine similarity well

cosine-similarity-expt

cpp_mmh3

dist-sim-metrics-using-fmh

Compute different metrics using FMH, and also without using sketch, and see the results

dn-ds-using-fracminhash

enviroscale

This is a code repository that is to be installed in a raspberry pi to make the pi headless.

extract-kegg-organisms

fall21algorithmsimplementations

Implementations of all algorithms taught in Fall 2021, 565: Algo Analysis and Design

fancy-mutation-model

A "non-simple" mutation model supporting insertion, deletion and substitutions

find_all_solutions

Find all solutions to a polynomial equation

find_scale_factor_cosine_fmh

Find an appropriate scale factor for estimating cosine similarity using FracMinHash sketch

fmm

Fancy mut model

frac_kmc

KMC modified to compute FMH sketches (hopefully)

fununifrac

gtdb-read-and-extract

Manually downloaded the .tree file from GTDB. Using bacteria tree. Then, starting with a random species, selected genomes that are at the same species, family, genus, order, phylum etc. Then, extracted pairwise distances from the entire taxonomy tree, and then computed tree off of those pairwise distances using neighbor joining.

guidescan-cli

A gRNA database generation tool.

hello_world

This is my "Hello Wrld" project.

implementation-of-a-simple-raster-based-pipeline

This is an implementation of a simple Raster-based graphics pipeline.

iot_actuation_commands

# Commands

k-means-clustering-on-2-dimensional-data-points-with-visual-representation

This project implements the K-means clustering algorithm on a set of 2D data points.