Akhilesh Kaushal's repositories
ntEdit
✏️ Genome assembly polishing & SNV detection
pwiz
The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
MsdialWorkbench
Universal workbench incorporating msdial, msfinder, and mrmprobs
oktoberfest
Rescoring and spectral library generation pipeline for proteomics.
goldrush
Linear-time de novo Long Read Assembler
btllib
Bioinformatics Technology Lab common code library
RNA-Bloom
:hibiscus: reference-free transcriptome assembly for short and long reads
RNA-Scoop
:shipit: interactive visualization of single-cell transcriptomes
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.
LongStitch
Correct and scaffold assemblies using long reads
DRAGMAP
DRAGEN open-source mapper
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
transabyss
de novo assembly of RNA-seq data using ABySS
SpliceAI
A deep learning-based tool to identify splice variants
Metabolomics-I
Untargeted LC/MS-based metabolomics data analysis.
mirna
microRNA profiling pipeline
SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
CITE-seq_optimization
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
MOFA2
Multi-Omics Factor Analysis V2 (MOFA+)
skylab
Secondary analysis pipelines
scRNAseq_Benchmark
Bench-marking classification tools for scRNA-seq data
aws-cli
Universal Command Line Interface for Amazon Web Services
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.
immunarch
immunarch: An R Package for Painless Bioinformatics Analysis of T-cell and B-cell Immune Repertoire Data
gatk-docs
Documentation archive for GATK tools and workflows