Arjun Biddanda's repositories
aabiddanda.github.io
Personal Website
snakemake_demo
Demo repo for new cluster setup with snakemake (excludes configs)
smcpp_bootstrap
Pipeline for running SMC++ on WGS data.
comp_bio_demo_2024
Demo for skype a scientist activity 2024
AmpliCoNE-tool
AmpliCoNE: Ampliconic Copy Number Estimator
xsmc
Exact decoding of the sequentially Markov coalescent.
geosfs_empirical
Obtaining annotated SFS from publicly available datasets across multiple populations
bth
scripts for heteroskedastic tests
rMCMC
Recombination MCMC
stdpopsim
A library of standard population genetic models
tszip
Gzip-like compression for tskit tree sequences
demes-python
Tools for describing and manipulating demographic models.
poibin
Poisson Binomial Probability Distribution for Python
makeScaffold
Build a haplotype scaffold for a VCF/BCF from a PED file
Cannings_Model_Approximations
Investigating deviations from the Coalescent in the Moran Model
emeraLD
tools to efficiently retrieve and calculate LD
sublinear-Li-Stephens
Calculates the probability of a haplotype given a population reference panel
geovar_rep_paper
Repository to replicate results from the GeoVar paper
project_template
Template for project directories to make sure code is standardized
gdc
Short scripts for converting genetic data between formats.
fiveMinuteStats
A repo of short "vignettes" illustrating statistical concepts; http://stephens999.github.io/fiveMinuteStats/analysis/