Pinned Repositories
KEGG_sketching_annotation
Scripts to sketch KEGG and explore using FracMinHash as a way to functionally annotate a metagenome
mutation-rate-ci-calculator
This software calculates a confidence interval for the mutation rate from a set of observed containment indices under a simple nucleotide mutation process.
Artificial-Neural-Network-based-Image-Classifier
Implementation of a neural network from scratch by coding the backpropagation algorithm.
dist-sim-metrics-using-fmh
Compute different metrics using FMH, and also without using sketch, and see the results
dn-ds-using-fracminhash
fancy-mutation-model
A "non-simple" mutation model supporting insertion, deletion and substitutions
frac_kmc
KMC modified to compute FMH sketches (hopefully)
kRISP-mER
A tool to generate personalized guide RNAs for CRISPR without using a reference genome
phylogenetic-tree-using-fracminhash
This repo can be thought of as a counterpart to Mashtree - which computes a tree based off of Mash distance. Instead, in this repo, we build a tree based off of FracMinHash distance.
sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
mahmudhera's Repositories
mahmudhera/kRISP-mER
A tool to generate personalized guide RNAs for CRISPR without using a reference genome
mahmudhera/dist-sim-metrics-using-fmh
Compute different metrics using FMH, and also without using sketch, and see the results
mahmudhera/fancy-mutation-model
A "non-simple" mutation model supporting insertion, deletion and substitutions
mahmudhera/frac_kmc
KMC modified to compute FMH sketches (hopefully)
mahmudhera/annotate_genomes_with_ncbi_taxid
mahmudhera/cami_ani_binning
Using ani calculated using FracMinHash, this repository will assign contigs to bins. Data collected from the CAMI website.
mahmudhera/compare-constants-in-cosine-proof
Comparing a few constants that mathematically showed up in the proof of cosine similarity
mahmudhera/compare_ground_truths
mahmudhera/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
mahmudhera/cosine-similarity-expt
mahmudhera/cpp_mmh3
mahmudhera/extract-kegg-organisms
mahmudhera/find_all_solutions
Find all solutions to a polynomial equation
mahmudhera/fmm
Fancy mut model
mahmudhera/FunUniFrac
mahmudhera/kegg-ko-annotation
mahmudhera/KEGG-sketch-each-KO
KEGG sketching and functional annotation using the "sketch each KO" approach
mahmudhera/KEGG_sketching_annotation
Scripts to sketch KEGG and explore using FracMinHash as a way to functionally annotate a metagenome
mahmudhera/KMC
Fast and frugal disk based k-mer counter
mahmudhera/kripmer_experiments_rerun
mahmudhera/krispmer-expreminets
Codes of all experiments to prepare results are in this repository, along with comments
mahmudhera/mahmudhera
Config files for my GitHub profile.
mahmudhera/parse_nominations
mahmudhera/process_sam_bam
mahmudhera/profiler_example
mahmudhera/python_multiprocessing_example
Example of python multiprocessing with shared global data and return queue for future references
mahmudhera/qual-exams
mahmudhera/Ray-tracer
Ray tracing based image generator
mahmudhera/run_camisim
Python wrapper to run camisim simulations. To be used in the "fast accurate metagenomic functional profiler" project
mahmudhera/YACHT
A rigorous hypothesis test for organism presence/absence in a metagenome