Aakrosh Ratan's repositories
ascat
ASCAT copy number R package
BioMine
Bioinformatics data-mining
biotools
Scripts and pipelines for internal use
covid-19-data
An ongoing repository of data on coronavirus cases and deaths in the U.S.
CrossMap
CrossMap is a python program to lift over genome coordinates from one genome version to another.
dotfiles
Configuration files for a fresh installation
dpviz
Visualize read depth from a GATK vcf file
graphtyper
Population-scale genotyping using pangenome graphs
HLA-LA
Fast HLA type inference from whole-genome data
mediabuilder
Author your academic documents in markdown
MultiK
MultiK is a data-driven tool that objectively assesses the optimal number(s) of clusters based on the concept of consensus clustering via a multi-resolution perspective.
nanopore_assembly_and_polishing_assessment
Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of assembly and polishing
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
NIPTeR
R Package for Non Invasive Prenatal Testing (NIPT) analysis
parliament2
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
reveal.js
The HTML Presentation Framework
rna_seq_lesson
Website for "Introduction to RNA-Seq analysis, Fall 2023" at https://aakrosh.github.io/rna_seq_lesson/
SLAPenrich
Sample Level Analysis of Pathway Alteration Enrichments
svtyper
Bayesian genotyper for structural variants
telseq
A software for calculating telomere length
UCSC_LURE
LURE (Learning UnRealized or Events Using Supervised Machine Learning)