novartis Goto Github PK
Type: Organization
Location: Cambridge, MA
Type: Organization
Location: Cambridge, MA
Data and Code for publication titled “Patient brain organoids identify a link between the 16p11.2 copy number variant and the RBFOX1 gene”
MHC-II presentation predictor
Parse a simplified JSONPath-like syntax
Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms
This repository contains code examples for several methods in a Causal Inference in RCTs short course.
Iba1+ cells in the PEC are generally sparsely distributed around the posterior eye cup, but manual quantification of these cells is time consuming. Therefore we developed a second semi-automated MatLab code to quantify single Iba1+ cells. The operator is presented with masked, randomized images and allowed to remove non-specific fluorescence (false positive) and/or add missed cells (false negative) to the analysis. The MatLab code is based on size and intensity gating. Objects that have more signal than the background, and are in the size parameters are quantified. The parameters can be adjusted to meet other quantification needs.
Analysis scripts and processed data for CELL-REPORTS-D-21-02389R3
CellSIUS: Cell Subtype Identification from Upregulated gene Sets
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures
Confluent and overlapping cells are difficult to quantify in low power images. This MatLab code allows a user to analyze the pixel intensity (integrated density) over a region of interest (ROI) in low power images as a surrogate for cell number. This code was optimized for use in our Choroidal Neovascularization model, and allows for the analysis of three ROIs per image. Both the intensity gate and the radius of ROI's can be changed to meet the needs of the project.
By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively facilitated
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.
This code allows is for diversity picking across multiple different, and potentially overlapping chemical compound classes, while at the same time optimizing a property score. This algorithm has been used in the re-design of the Novartis screening deck as described in https://dx.doi.org/10.1021/acs.jmedchem.0c01332
Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencing
An R-package for performing dynamic path analysis on survival data with estimation of the corresponding direct, indirect, and total effects.
DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline
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"
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.
Unix-based RNA-seq quantification pipeline
Unix based RNA-seq quantification module
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
FRPipe: A 19F NMR data analysis pipeline
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
GridVar is a jQuery plugin that visualizes multi-dimensional datasets as layers organized in a row-column format.
"Where files live" - Simple object management system using AWS S3 and Elasticsearch Service to manage objects and their metadata
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.