novartis Goto Github PK

16p11.2-organoid-scrna-seq

Data and Code for publication titled “Patient brain organoids identify a link between the 16p11.2 copy number variant and the RBFOX1 gene”

advanced-user-interfaces-for-shiny-developers

aegis

MHC-II presentation predictor

attrib-path

Parse a simplified JSONPath-like syntax

bamdd

Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms

causal-inference-in-rcts

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

cell-quant

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.

cell-reports-d-21-02389r1

Analysis scripts and processed data for CELL-REPORTS-D-21-02389R3

cellsius

CellSIUS: Cell Subtype Identification from Upregulated gene Sets

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.

chembiomultimodalautoencoders

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

chess-redux

cnv-analysis

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.

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.

div_rank

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

dms-pipeline

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

dpasurv

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

drug-seq

DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline

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.

eqp-cluster

Unix-based RNA-seq quantification pipeline

eqp-qm

Unix based RNA-seq quantification module

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

frpipe

FRPipe: A 19F NMR data analysis pipeline

granulator

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

gridvar

GridVar is a jQuery plugin that visualizes multi-dimensional datasets as layers organized in a row-column format.

habitat

"Where files live" - Simple object management system using AWS S3 and Elasticsearch Service to manage objects and their metadata

hdf5r

hpath

An ontology of histopathological morphologies

jaeger

JAEGER is a deep generative approach for small-molecule design