Novartis

Novartis

Geek Repo

Location:Cambridge, MA

Home Page:https://opensource.nibr.com

Github PK Tool:Github PK Tool

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.

Language:PythonLicense:Apache-2.0Stargazers:51Issues:12Issues:59

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

Language:HTMLLicense:NOASSERTIONStargazers:39Issues:4Issues:21

pisces

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Language:PythonLicense:Apache-2.0Stargazers:28Issues:2Issues:20

pqsar2cpd

pqsar2cpd is a deep learning algorithm for translation of activity profiles into novel molecules.

Language:PythonLicense:MITStargazers:28Issues:5Issues:2

ChemBioMultimodalAutoencoders

a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures

Language:PythonLicense:MITStargazers:26Issues:7Issues:2

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.

Language:HTMLLicense:GPL-3.0Stargazers:26Issues:5Issues:0

xgx

Exploratory Graphics for PKPD data

Causal-inference-in-RCTs

This repository contains code examples for several methods in a Causal Inference in RCTs short course.

Language:RLicense:MITStargazers:15Issues:4Issues:0

xgxr

R package for supporting exploratory graphics at http://opensource.nibr.com/xgx

Language:RLicense:NOASSERTIONStargazers:13Issues:8Issues:32

RBesT

Tool-set to support Bayesian evidence synthesis in R

Language:RLicense:GPL-3.0Stargazers:12Issues:4Issues:4

AEGIS

MHC-II presentation predictor

Language:PythonLicense:BSD-3-ClauseStargazers:9Issues:4Issues:0

dms-pipeline

Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencing

Language:PythonLicense:MITStargazers:5Issues:4Issues:0

verifyr

A package to hold R functions for comparing different version of clinical trial TLFs

Language:Rich Text FormatLicense:MITStargazers:4Issues:1Issues:8

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

Language:Jupyter NotebookLicense:MITStargazers:3Issues:2Issues:0

NDSRIs_in_silico_tool

N-nitrosamine Autonomous Carcinogenic Potency Categorization Approach Calculation Tool

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:3Issues:3Issues:0

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.

Language:RLicense:NOASSERTIONStargazers:3Issues:3Issues:0

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.

Language:PythonLicense:Apache-2.0Stargazers:3Issues:2Issues:0

Novartis.github.io

Public gallery of NIBR Open Source projects

Language:HTMLStargazers:2Issues:5Issues:0

dpasurv

An R-package for performing dynamic path analysis on survival data with estimation of the corresponding direct, indirect, and total effects.

Language:RLicense:MITStargazers:1Issues:1Issues:0

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.

Language:RLicense:MITStargazers:1Issues:3Issues:0

FRPipe

FRPipe: A 19F NMR data analysis pipeline

Language:PythonLicense:MITStargazers:0Issues:2Issues:0

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.

Language:RLicense:GPL-3.0Stargazers:0Issues:2Issues:0

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

Language:Jupyter NotebookLicense:MITStargazers:0Issues:1Issues:0

Kepler

This package converts GeoJSON annotations into GeoPandas polygons for AnnData h5df data structures.

Language:Jupyter NotebookLicense:MITStargazers:0Issues:3Issues:0

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)

Language:RLicense:MITStargazers:0Issues:0Issues:0

monitOS

Monitoring overall survival in pivotal trials for indolent cancer

Language:RLicense:MITStargazers:0Issues:0Issues:0

px_tmt_daa

Differential abundance analysis of proteomics (TMT) data

License:MITStargazers:0Issues:2Issues:0

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

Language:PythonLicense:MITStargazers:0Issues:3Issues:0

TF_Prioritization_Benchmark_GB2023

Code to reproduce the paper figures from TF prioritization tool outputs.

License:MITStargazers:0Issues:2Issues:0