Pinned Repositories
ascat
ASCAT copy number R package
BAMreport
Report on a BAM file
BioMine
Bioinformatics data-mining
CNVTk
Call CNVs based on read-depth signal.
dbAssign
Assign sequences to reference genomes in a database
ldtools
Analyze the patterns of linkage disequilibrium
YASRA
Reference based assembler
BaitSTR
Automate the discovery of exact short tandem repeats (and its flanking region) from Illumina fastq sequences.
DIAL
De novo Identification of Alleles
indelMINER
Identify indels from BAM files.
aakrosh's Repositories
aakrosh/BAMreport
Report on a BAM file
aakrosh/ldtools
Analyze the patterns of linkage disequilibrium
aakrosh/ascat
ASCAT copy number R package
aakrosh/BioMine
Bioinformatics data-mining
aakrosh/biotools
Scripts and pipelines for internal use
aakrosh/CharGer
Characterization of Germline variants
aakrosh/covid-19-data
An ongoing repository of data on coronavirus cases and deaths in the U.S.
aakrosh/CrossMap
CrossMap is a python program to lift over genome coordinates from one genome version to another.
aakrosh/dotfiles
Configuration files for a fresh installation
aakrosh/dpviz
Visualize read depth from a GATK vcf file
aakrosh/graphtyper
Population-scale genotyping using pangenome graphs
aakrosh/HLA-LA
Fast HLA type inference from whole-genome data
aakrosh/lastz
Program for aligning DNA sequences, a pairwise aligner.
aakrosh/mediabuilder
Author your academic documents in markdown
aakrosh/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.
aakrosh/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
aakrosh/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
aakrosh/NIPTeR
R Package for Non Invasive Prenatal Testing (NIPT) analysis
aakrosh/parliament2
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
aakrosh/reveal.js
The HTML Presentation Framework
aakrosh/rna_seq_lesson
Website for "Introduction to RNA-Seq analysis, Fall 2023" at https://aakrosh.github.io/rna_seq_lesson/
aakrosh/scarHRD
aakrosh/Segmentum
Segmentum a fast tool for copy number analysis of cancer genome
aakrosh/SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
aakrosh/SLAPenrich
Sample Level Analysis of Pathway Alteration Enrichments
aakrosh/SRTk
Find the best split alignments for reads that carry signatures of SVs.
aakrosh/svtyper
Bayesian genotyper for structural variants
aakrosh/SVXplorer
Structural Variant Caller
aakrosh/telseq
A software for calculating telomere length
aakrosh/UCSC_LURE
LURE (Learning UnRealized or Events Using Supervised Machine Learning)