Akhilesh Kaushal's repositories
aws-batch-user-guide
The open source version of the AWS Batch user guide. You can submit feedback & requests for changes by submitting issues in this repo or by making proposed changes & submitting a pull request.
Targeted_transcriptomics
Mair and Erickson, A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level
bowtie2
A fast and sensitive gapped read aligner
CITE-seq-Count
A tool that allows to get UMI counts from a single cell protein assay
cpython
The Python programming language
single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
handson-ml
A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in python using Scikit-Learn and TensorFlow.
cytof-workflow-v3
CyTOF workflow. Version 3.
SingleR
Clone of the Bioconductor repository for the SingleR package.
liger
R package for integrating and analyzing multiple single-cell datasets
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
CSV-to-FCS
A short script for converting .csv file data into an .fcs file, and vise versa.
airflow
Apache Airflow
Mammary_snATAC-seq
Single cell ATAC-seq of mouse mammary cells
encoded
Metadata database for ENCODE project
aws-batch-genomics
Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
CytoTools
Useful small scripts for cytometry data management
msproteomicstools
Some hopefully useful tools for mass spectrometry applied to proteomics
Python
All Algorithms implemented in Python
oneliners
Useful bash one-liners for bioinformatics.
The-Broad-Institute-Single-Cell-RNA-Seq-Data-Set
Visualize cancer genomes with FAIR single-cell RNA-seq data
clinvar-miner
Website to analyze conflicting assertions in ClinVar
scRNAseq_cell_cluster_labeling
Scripts to run and benchmark scRNA-seq cell cluster labeling methods
SPONGE
Sparse Partial correlation ON Gene Expression - an R package for fast and robust ceRNA network inference
bowtie-majref
Scripts related to building major-allele references for Bowtie and Bowtie 2