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    94 repositories

    • UNIQUE

      Public
      A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.
      machine-learningcalibrationuncertainty-quantification
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•14•1•0•Updated Oct 4, 2024Oct 4, 2024

    • risk_assessments

      Public
      Repository collecting risk assessment data on the packages installed on our Statistical Computing Environment at Novartis.
      MIT License
      •1•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • torchsurv

      Public
      Deep survival analysis made easy
      deep-learningpytorchsurvival-analysis
      Python
      •
      MIT License
      •7•57•4•0•Updated Oct 1, 2024Oct 1, 2024

    • chraw

      Public
      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.
      R
      •
      MIT License
      •2•5•0•0•Updated Sep 10, 2024Sep 10, 2024

    • beyond-PK-score

      Public
      Prediction of Small-Molecule Developability Using Large-Scale In Silico ADMET Models
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 8, 2024Sep 8, 2024

    • ChemicalSeriesReconstruction

      Public
      25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 8, 2024Sep 8, 2024

    • tidymodules

      Public
      An Object-Oriented approach to Shiny modules
      rshinycommunicationoopinheritanceshiny-modulestidy-operators
      R
      •
      Other
      •11•143•25•0•Updated Sep 5, 2024Sep 5, 2024

    • dpasurv

      Public
      An R-package for performing dynamic path analysis on survival data with estimation of the corresponding direct, indirect, and total effects.
      R
      •
      Other
      •0•1•0•0•Updated Aug 27, 2024Aug 27, 2024

    • DeepCt

      Public
      Predicting pharmacokinetic compartmental models and concentration-time curves from chemical structure using deep learning
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 26, 2024Aug 26, 2024

    • scar

      Public
      scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
      machine-learninggenerative-modelprobabilistic-graphical-modelsvariational-autoencodersingle-cell-rna-seqdenoising-algorithmcite-seqcrispr-screenpytorch
      Python
      •4•48•0•0•Updated Aug 17, 2024Aug 17, 2024

    • bamdd

      Public
      Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms
      clinicalbayesianstanbrms
      R
      •
      GNU General Public License v2.0
      •2•14•0•0•Updated Aug 5, 2024Aug 5, 2024

    • peakCombiner

      Public
      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.
      R
      •
      Other
      •2•4•0•2•Updated Jul 18, 2024Jul 18, 2024

    • Cu-Catalyzed-Ligands-Design

      Public
      By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively facilitated
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 27, 2024Jun 27, 2024

    • Causal-inference-in-RCTs

      Public
      This repository contains code examples for several methods in a Causal Inference in RCTs short course.
      R
      •
      MIT License
      •0•20•0•0•Updated Jun 7, 2024Jun 7, 2024

    • pisces

      Public
      PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
      bioinformaticsbioinformatics-pipelinernaseqtranscriptomicssalmonrnaseq-pipeline
      Python
      •
      Apache License 2.0
      •3•29•11•0•Updated May 28, 2024May 28, 2024

    • scOTGM

      Public
      This is the official codebase for "sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass Transport on the Manifold of Gaussian Mixtures"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 17, 2024May 17, 2024

    • WATCH

      Public
      An R-repository to implement a double robust version of the WATCH workflow published in Sechidis et al. (2024)
      R
      •
      MIT License
      •0•0•0•0•Updated May 17, 2024May 17, 2024

    • dWIZGenomics

      Public
      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"
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 2, 2024May 2, 2024

    • easyTrackHubs

      Public
      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.
      HTML
      •
      GNU General Public License v3.0
      •0•27•0•0•Updated Apr 29, 2024Apr 29, 2024

    • TF_Prioritization_Benchmark_GB2023

      Public
      Code to reproduce the paper figures from TF prioritization tool outputs.
      MIT License
      •0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • px_tmt_daa

      Public
      Differential abundance analysis of proteomics (TMT) data
      MIT License
      •0•0•0•0•Updated Apr 11, 2024Apr 11, 2024

    • monitOS

      Public
      Monitoring overall survival in pivotal trials for indolent cancer
      R
      •
      MIT License
      •1•0•0•1•Updated Apr 9, 2024Apr 9, 2024

    • knockoffs-cpt2024paper-simulations

      Public
      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)
      R
      •
      MIT License
      •0•1•0•0•Updated Mar 20, 2024Mar 20, 2024

    • cellxgene-gateway

      Public
      Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
      visualizationrna-seqdatavizscrna-seqscientifictranscriptomicsh5ad
      Python
      •
      Apache License 2.0
      •32•52•10•1•Updated Mar 10, 2024Mar 10, 2024

    • knockofftools

      Public
      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.
      R
      •
      MIT License
      •1•1•1•0•Updated Mar 4, 2024Mar 4, 2024

    • TAT

      Public
      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.
      Python
      •
      Apache License 2.0
      •1•3•0•0•Updated Jan 30, 2024Jan 30, 2024

    • RBesT

      Public
      Tool-set to support Bayesian evidence synthesis in R
      clinicalbayesianmeta-analysishistorical-data
      R
      •
      GNU General Public License v3.0
      •2•19•1•0•Updated Jan 8, 2024Jan 8, 2024

    • verifyr

      Public
      A package to hold R functions for comparing different version of clinical trial TLFs
      Rich Text Format
      •
      MIT License
      •5•4•5•0•Updated Jan 1, 2024Jan 1, 2024

    • dms-pipeline

      Public
      Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencing
      Python
      •
      MIT License
      •0•5•0•0•Updated Dec 15, 2023Dec 15, 2023

    • NDSRIs_in_silico_tool

      Public
      N-nitrosamine Autonomous Carcinogenic Potency Categorization Approach Calculation Tool
      Jupyter Notebook
      •
      Apache License 2.0
      •1•4•0•0•Updated Dec 13, 2023Dec 13, 2023