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ad_citation_network_analysis

Code for analyzing a citation network of papers related to Alzheimer's Disease

anchor_residuals

Minimum Example For Calculating Residuals From Anchor Screen Data

anchor_screen_nets

anchor_screen_parp_lfcs

anchor_screens_scripts

Scripts Used for Anchor Screen Manuscript

big_papi_paralogs

Analyze synthetic relationships between paralog genes in a Big Papi screen

bigpapi

notebooks for analyzing data from Najm, Fadi J., et al. "Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens." Nature biotechnology 36.2 (2018): 179.

cas12a_manuscript

Notebooks for the manuscript Optimization of AsCas12a for combinatorial genetic screens in human cells.

cell_embedding

Visualize maps of cancer cell lines

combibuild

Build combinatorial libraries for CRISPR screening

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

coronavirus_screen_analysis

dash-extensions

datavis_workshop

Broad CodeRATS' data visualization workshop

deck_of_cards

A minimal nbdev example

deployment-heroku

Deployment Heroku

depmap_clusters

Generate clusters of genes using depmap co-essentiality data

dnafeaturesviewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

en_pam_gb

examples

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

fastbook

Draft of the fastai book

fasts

flask-ml-app

Example project

ggpointdensity

:chart_with_upwards_trend: :bar_chart: Introduces geom_pointdensity(): A Cross Between a Scatter Plot and a 2D Density Plot.

gpp-guide-design

CRISPR sgRNA design for the Genetic Perturbation Platform at the Broad Institute

gpplotting

Plotting functions for the Genetic Perturbation Platform's R&D group at the Broad institute.

inftrn_lassoebic

Transcriptional regulatory network inference from gene expression and prior information with LASSO-EBIC or LASSO-CV

intactr

Calculate interaction scores from combinatorial screening data

mtl_julia

Multitask Learning for Transcriptional Regulatory Network Inference in Julia

opticalpooledscreens