CodingBash
Harvard PhD student in Bioinformatics & Integrative Genomics.
Harvard Medical SchoolBoston, MA
Pinned Repositories
CNV-Clinical-Preprocessing
Subset of scripts created during the CSHL URP 2018. Developing method to extract predictive biomarkers from PDAC patient derived organoids. Using COREs from CNV and WES data from pancreatic tumor organoids to predict chemotherapeutic drug response. This repository investigates copy number preprocessing tools and also preprocesses genomic features for ML analysis.
CRISPR-library-prep
Some helper functions for planning library prep for CRISPR screens
CRISPR-shrinkage
CRISPR-SURF
FlyCAGE
A modern web tool to find genes with similar expression
heart-disease-glm
Ordinal logistic regression of Cleveland Clinic Foundation heart disease dataset.
muse-monitor
Utilizing the Muse Headband to detect neurological and physical incidents of hospital patients
rna_mutect_cloud
Call somatic variants in bulk RNA-seq data in the cloud
CRISPR-Correct
Perform CRISPR guide mapping and analysis that considers protospace self-editing and surrogate sensor sequences. Self-editing aware mapping takes a hamming-distance approach unbiased by expectations in editing patterns.
CRISPR-millipede-target
Calculate the enrichment scores of CRISPR alleles and variants from direct target amplicon-sequencing data using Bayesian linear regression model "millipede".
CodingBash's Repositories
CodingBash/muse-monitor
Utilizing the Muse Headband to detect neurological and physical incidents of hospital patients
CodingBash/CNV-Clinical-Preprocessing
Subset of scripts created during the CSHL URP 2018. Developing method to extract predictive biomarkers from PDAC patient derived organoids. Using COREs from CNV and WES data from pancreatic tumor organoids to predict chemotherapeutic drug response. This repository investigates copy number preprocessing tools and also preprocesses genomic features for ML analysis.
CodingBash/FlyCAGE
A modern web tool to find genes with similar expression
CodingBash/heart-disease-glm
Ordinal logistic regression of Cleveland Clinic Foundation heart disease dataset.
CodingBash/rna_mutect_cloud
Call somatic variants in bulk RNA-seq data in the cloud
CodingBash/bash-personal-site
Basheer's Personal Site
CodingBash/CRISPR-library-prep
Some helper functions for planning library prep for CRISPR screens
CodingBash/CRISPR-shrinkage
CodingBash/CRISPR-SURF
CodingBash/ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
CodingBash/bmif_pset1
CodingBash/cellx-postcomfirmation-pg-layer
AWS Lambda Node.JS layer containing postegresql package for the AWS Cognito Post-Confirmation trigger
CodingBash/Concrete-Autoencoders
CodingBash/CRISPR-BE-Sensor
Parsing of Sherwood BE-Sensor amplicon-seq FASTQs
CodingBash/CRISPR-be-sensor-deprecated
Deprecated. See CRISPR-ambiguous-mapping for mapping code
CodingBash/crispr-millipede-coding
CodingBash/crispr_pegrna_design
CodingBash/docker-anaconda-bioinformatics-tools
CodingBash/docker-python-bioinformatics-tools
Docker image for python bioinformatics libraries
CodingBash/fastapi-realworld-example-app
Backend logic implementation for https://github.com/gothinkster/realworld with awesome FastAPI
CodingBash/glmpca
CodingBash/manim_examples
CodingBash/millipede
A library for bayesian variable selection
CodingBash/notebook_examples
CodingBash/PE_SupplementaryCode
Supplementary Code for Kim et al. Nature Biotechnology 2020
CodingBash/perturb-tools
Utility package for bulk/single-cell CRISPR screens
CodingBash/Phoneword_iOS_Tutorial
Learning cross-platform development. Xamarin tutorial from https://docs.microsoft.com/en-us/xamarin/ios/get-started/hello-ios/hello-ios-quickstart?pivots=macos
CodingBash/resVAE
resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.
CodingBash/RNA_MUTECT_1.0-1
CodingBash/wot
A software package for analyzing snapshots of developmental processes