Pinned Repositories
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cellxgene-gateway
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
ontobrowser
OntoBrowser is a web-based application for managing ontologies
peax
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
pQSAR
Massively multitask stacked model for predicting activity of thousands of biological assays
scar
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
shinyValidator
Audit your Shiny apps at each commit. Multiple levels of testings are offered: startup and crash tests, performance tests (load test and global code profiling), reactivity audit as well as output tests. All results are gathered in an HTML report uploaded and available to everyone on any CI/CD plaform or RStudio Connect
tidymodules
An Object-Oriented approach to Shiny modules
torchsurv
Deep survival analysis made easy
YADA
Open-source Data Ops
Novartis's Repositories
Novartis/tidymodules
An Object-Oriented approach to Shiny modules
Novartis/torchsurv
Deep survival analysis made easy
Novartis/cellxgene-gateway
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
Novartis/scar
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
Novartis/pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
Novartis/easyTrackHubs
This package provides a function to reformat lists of genome coverage files, such as bigWig of bam files, into the directory structure of a UCSC Track Hub ready to be visualized in the genome browser. For details about it's use, please have a look at the vignette of the package.
Novartis/Causal-inference-in-RCTs
This repository contains code examples for several methods in a Causal Inference in RCTs short course.
Novartis/UNIQUE
A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.
Novartis/RBesT
Tool-set to support Bayesian evidence synthesis in R
Novartis/bamdd
Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms
Novartis/chraw
The package analyzes chromatin and multi-omic experiments. It extends the MultiAssayExperiment object and builds a ChrawExperiment object from ENCODE’s output. It performs QC plotting, identifies differential events and other functionalities. More details in package vignettes.
Novartis/dms-pipeline
Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencing
Novartis/peakCombiner
The fully R based tool peakCombiner is a user-friendly, transparent, modular and customizable package with the purpose to create a consensus peak file from genomic input regions. The aim is to allow even novice R users to create good quality combined peak sets to be used as the starting point for most downstream differential analyses.
Novartis/rdocx
Create and edit reporting documents using R
Novartis/TAT
Transcriptomics-to-Activity Transformer (TAT) is a deep learning model to predict compound bioactivity in a dose-response assay using compound-induced transcriptomic profiles over concentration.
Novartis/verifyr
A package to hold R functions for comparing different version of clinical trial TLFs
Novartis/DeepCt
Predicting pharmacokinetic compartmental models and concentration-time curves from chemical structure using deep learning
Novartis/Cu-Catalyzed-Ligands-Design
By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively facilitated
Novartis/dpasurv
An R-package for performing dynamic path analysis on survival data with estimation of the corresponding direct, indirect, and total effects.
Novartis/knockoffs-cpt2024paper-simulations
An R-repository to run simulation studies as in the paper 'All that glitters is not gold: Type-I error controlled variable selection from clinical trial data' by Zimmermann et al. (2024)
Novartis/knockofftools
An R-package containing a suite of knockoffs functions and methods from existing R-packages and the knockoffs literature. Some of the R functions are novel implementations of recent methods.
Novartis/risk_assessments
Repository collecting risk assessment data on the packages installed on our Statistical Computing Environment at Novartis.
Novartis/monitOS
Monitoring overall survival in pivotal trials for indolent cancer
Novartis/beyond-PK-score
Prediction of Small-Molecule Developability Using Large-Scale In Silico ADMET Models
Novartis/ChemicalSeriesReconstruction
25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution
Novartis/dWIZGenomics
Provides the code used to reproduce the figures containing the genomic data for the publication "A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction"
Novartis/px_tmt_daa
Differential abundance analysis of proteomics (TMT) data
Novartis/scOTGM
This is the official codebase for "sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass Transport on the Manifold of Gaussian Mixtures"
Novartis/TF_Prioritization_Benchmark_GB2023
Code to reproduce the paper figures from TF prioritization tool outputs.
Novartis/WATCH
An R-repository to implement a double robust version of the WATCH workflow published in Sechidis et al. (2024)