Genentech/epiregulon

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R
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Created almost 2 years ago
Updated 10 months ago

Genentech/epiregulon

Genentech

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Construct gene regulatory networks and infer transcription factor (TF) activity in single cells by integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data.

gReLU

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

equifold

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

scimilarity

A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.

pviz

sVAE

walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)

iterative-perturb-seq

Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors

Jupyter Notebook

polygraph

Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of regulatory elements.

Jupyter Notebook

regLM

Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.

Jupyter Notebook

dcdfg

covtracer

Tools for contextualizing tests, built using covr test traces.

jmpost

Absolve

Absolve antibody variable domain sequence analysis

psborrow2

psborrow2: Bayesian Dynamic Borrowing Simulation Study and Analysis

ringer

RINGER: Rapid Conformer Generation for Macrocycles with Sequence-Conditioned Internal Coordinate Diffusion

beignet

A standard library for biological research.

GraphGUIDE

Jupyter Notebook

Isosceles

The Isoforms from Single-Cell; Long-read Expression Suite

midasHLA

R package enabling statistical association analysis and using immunogenetic data transformation functions for HLA amino acid fine mapping, analysis of HLA evolutionary divergence as well as HLA-KIR interactions.

GameRank

gPKPDviz

Perturb-OT

Cross-modality matching and prediction with labeled Gromov-Wasserstein Optimal Transport.

Jupyter Notebook

nodags-flows

Jupyter Notebook

branched-diffusion

Jupyter Notebook

SASS

rd2markdown

uniprot-mongodb

uniprot-js

cremp

CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning

multiGroupVI

Jupyter Notebook

fishtones-js

Islander

Jupyter Notebook

battery

Architecture framework for Shiny Apps

FacileDataSet

A fluent API for accessing multi-assay high-throughput genomics data.

bandwidth-graph-generation

data-detective

contrastive-ops

Jupyter Notebook

g_ani

Isosceles_Paper

pviz-app-vep

pviz-app-proteomics-3d

topological_PRM_for_lungHRCT

Lung image analysis pipeline for topological PRM maps

phase1b

spex_frontend

genentech.github.io

ConMedClassify

Process clinical ADaM-format data and classify subjects into profiles based on their concomitant medication usage within a clinical trial.

cancer-sc-embed

Jupyter Notebook

spex_demo

t_opt

cdd_chem