kgori

Pinned Repositories

evolsim
Student evolution paper exercise
Language:Go00
GTP
Megan Owen and Scott Provan's java implementation of their GTP algorithm for calculating the geodesic distance between phylogenetic trees
Language:Java34
phylo_utils
Likelihood calculation utilities - pruning algorithm, phylogenetic models...
Language:Python00
pllpy
Python wrapper for the phylogenetic likelihood library (PLL), from the Exelixis lab. Of RAxML fame.
Language:C++42
python_tools_on_github
Some useful bioinformatics / phylogenetics python code that I've written and sometimes even use
Language:Python74
scluster
An implementation of the self-tuning spectral clustering algorithm described in Zelnik-Manor and Perona (2004)
Language:Python11 3 00
sigfit
Flexible Bayesian inference of mutational signatures
Language:R33 5 608
tree_distance
Implementation of geodesic, Robinson-Foulds and Euclidean tree distance metrics
Language:C++3 3 21
treeCl
Clustering phylogenetic trees with python
Language:C++25 6 2712
Mixed
Repo of simple scripts used by TCG
Language:C++01

kgori's Repositories

kgori/sigfit
Flexible Bayesian inference of mutational signatures
Language:R33 5 608
kgori/treeCl
Clustering phylogenetic trees with python
Language:C++25 6 2712
kgori/tree_distance
Implementation of geodesic, Robinson-Foulds and Euclidean tree distance metrics
Language:C++3 3 21
kgori/nf_population_genetics
Nextflow pipeline for running population genetics analysis to accompany cancer horizontal transfer paper
Language:R1
kgori/phylo_utils
Likelihood calculation utilities - pruning algorithm, phylogenetic models...
Language:Python00
kgori/.doom.d
Emacs config files
Language:Emacs Lisp
kgori/alco
Allele counter-alike
Language:Rust
kgori/binned_median
Online algorithm for computing median of a stream of non-negative integers, with low memory requirements
Language:C++2 0
kgori/boids
Boids flocking algorithm, using SFML
Language:C++
kgori/cellular_automaton
Game of life (+others) with SFML
Language:C++2 0
kgori/cnpipe
R package for copy number analysis
Language:R
kgori/copynumber_calling_pipeline
Language:R
kgori/directed_graph
Data structure from Professional C++ 5th ed.
Language:C++
kgori/gentools
Some convenience tools for genomic data
Language:Rust
kgori/json_parser
JSON parser built with Python
kgori/nextflow_demo
Lab meeting nextflow demo
Language:Nextflow
kgori/nf_ancestral_inference
Nextflow pipeline for running ancestral inference section of transmissible cancer horizontal transfer analysis
Language:R
kgori/nf_htrnaseq
Nextflow pipeline for horizontal transfer in CTVT RNAseq analysis
Language:R
kgori/pb_genotyper
Long read genotyping - nuclear horizontal transfer project
Language:Rust
kgori/Platypus
Platypus Variant Caller
Language:Cython
kgori/raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
kgori/region_counter
Counts the number of reads in an RNAseq alignment file in the categories Mapped, Mapped(exon) and Unmapped
Language:Rust
kgori/rngs
Toy implementations of Random Number Generators
Language:C++
kgori/rust-bwa
Rust wrapper of the BWA C API
Language:Rust1 0
kgori/segmentation
PCF and MultiPCF algorithms for segmenting sequence data - derived from R:copynumber, but written in C++
Language:C++
kgori/snv_analysis_pipeline
Workflow for post-processing of Somatypus variants
Language:R
kgori/somatypus
A Platypus-based variant calling pipeline for cancer data
Language:Python
kgori/somatypus_nf
Integrate Somatypus variant calling pipeline into Nextflow
Language:Python
kgori/strings_and_things
Common string algorithms, for learning
Language:C++
kgori/vcf_to_fasta
Program to extract a fasta alignment from mitochondrial variants in VCF format
Language:Rust1 0