Akhilesh Kaushal's repositories
amazon-ec2-user-guide-windows
The open source version of the Amazon EC2 User Guide for Windows. To submit feedback or requests for changes, submit an issue or make changes and submit a pull request.
AMPL
The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.
btllib
Bioinformatics Technology Lab common code library
CITE-seq_optimization
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
DRAGMAP
DRAGEN open-source mapper
gatk-docs
Documentation archive for GATK tools and workflows
goldrush
Linear-time de novo Long Read Assembler
immunarch
immunarch: An R Package for Painless Bioinformatics Analysis of T-cell and B-cell Immune Repertoire Data
LongStitch
Correct and scaffold assemblies using long reads
Metabolomics-I
Untargeted LC/MS-based metabolomics data analysis.
mirna
microRNA profiling pipeline
MOFA2
Multi-Omics Factor Analysis V2 (MOFA+)
MsdialWorkbench
Universal workbench incorporating msdial, msfinder, and mrmprobs
ntEdit
✏️ Genome assembly polishing & SNV detection
oktoberfest
Rescoring and spectral library generation pipeline for proteomics.
prosit
Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7
pwiz
The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
RNA-Bloom
:hibiscus: reference-free transcriptome assembly for short and long reads
RNA-Scoop
:shipit: interactive visualization of single-cell transcriptomes
scRNAseq_Benchmark
Bench-marking classification tools for scRNA-seq data
skylab
Secondary analysis pipelines
SpliceAI
A deep learning-based tool to identify splice variants
transabyss
de novo assembly of RNA-seq data using ABySS