Novartis's repositories
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.
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
ChemBioMultimodalAutoencoders
a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures
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.
Causal-inference-in-RCTs
This repository contains code examples for several methods in a Causal Inference in RCTs short course.
dms-pipeline
Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencing
GreyChemicalMatter
A pipeline to identify bioactive small molecules with likely novel modes of actions and dynamic SAR from historic cell-HTS profiles, with an example application and hitlist from PubChem data
NDSRIs_in_silico_tool
N-nitrosamine Autonomous Carcinogenic Potency Categorization Approach Calculation Tool
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.github.io
Public gallery of NIBR Open Source projects
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.
Data-Sharing-Technology-Assessment-Framework
DSTAF (Data Sharing Technology Assessment Framework) is an R Shiny app developed to support stakeholders in their evaluation of technologies and approaches that advance their data-sharing initiatives, whether they are interested in technologies for external data sharing or support an organization's internal data reuse.
Expressed_barcode_with_scRNAseq
ode repo for the manuscript titled Expressed Molecular Barcoding Coupled with Single Cell RNAseq Enables a High Resolution Investigation into the Evolution of Drug Tolerance
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)
monitOS
Monitoring overall survival in pivotal trials for indolent cancer
px_tmt_daa
Differential abundance analysis of proteomics (TMT) data
RescaleSTx
This is a package for rescaling coordinates for Visium 10x transcriptomics datasets. This enables the highest resolution (or an arbitrary resolution) of microscopy image to be used for STx analysis, which enables advanced image processing and machine-learning using image features and coordinates of spatial transcriptomics datasets
TF_Prioritization_Benchmark_GB2023
Code to reproduce the paper figures from TF prioritization tool outputs.