Avinash R's repositories
indian-newspaper-article-corpus
A corpus of newspaper articles from thehindu.com
duc-newspaper-analysis
Newspaper analysis
civic-api-client
Example tools using the CIVIC API
bam-parser-tutorial
A simple example of parsing BAM files using htslib
GenVisR
Genome data visualizations
hs37d5
Testing "git lfs"
templates
Templates for empty-files in different languages. Vim can be used to initialize a new file with these templates.
breakdancer
SV detection from paired end reads mapping
kallisto
Near-optimal RNA-Seq quantification
htslib
C library for high-throughput sequencing data formats
all1_panel_plots
A series of scripts to make panel plots for CNVs and regions of LOH across the genome.
CSE232
Course notes for CSE 232 at Washington University
svviz
Read visualizer for structural variants
genome-db-tgi-cancer-annotation-data
Unofficial repo for software vendoring or packaging purposes
gms
The Genome Modeling System installer (BETA).
alderman-vote-tracker
Board of Alderman Vote Tracker for City of St. Louis
samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
hiakoro
For generating choropleths of the US with Alaska and Hawaii
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.
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.'
denovogear-VNTR-code
denovogear-VNTR-code
denovogear-bb
denovo caller using beta binomial likelihoods
kmerCALL
kmerCALL