Pinned Repositories
arnav
Mutation calling using a site-specific binomial model
bam-parser-tutorial
A simple example of parsing BAM files using htslib
castools
Command line tool for the CAS project
common_scripts_GBlab
DEPRECATED
denovogear-legacy
Statistical model to detect de-novo mutations using sequencing data from trios and pairs.
fdr
Control the false discovery rate using the Benjamini Hochberg procedure in C++
gzip_reader
An example for reading gzipped files in C++
maury
An R package to detect sample-swaps in Next Generation Sequencing(NGS) data.
mpileup2readcounts
Get per-nucleotide readcounts from samtools mpileup
gatoravi's Repositories
gatoravi/hiakoro
For generating choropleths of the US with Alaska and Hawaii
gatoravi/DNG_BetaBinomial_Paired
DeNovoGear with BetaBinomial likelihoods for paired sample mutation calling. For example this package can be used to do tumor vs normal comparisons. The BetaBinomial likelihood model has been shown to have a higher sensitivity and specificity compared to the binomial model.
gatoravi/MFAST
Code accompanying this paper - 'A scalable method for identifying frequent subtrees in sets of large phylogenetic trees - Avinash Ramu, Tamer Kahveci and J Gordon Burleigh.'
gatoravi/simple-cv
A simple easily modifyable LaTeX documenclass to create academic CVs.
gatoravi/denovogear-VNTR-code
denovogear-VNTR-code
gatoravi/denovogear-bb
denovo caller using beta binomial likelihoods
gatoravi/kmerCALL
kmerCALL
gatoravi/seqerror
gatoravi/gatorADD
gatoravi/RandomAdd
gatoravi/common_scripts_GBlab
DEPRECATED