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  1. tidymodules tidymodules Public

    An Object-Oriented approach to Shiny modules

    R 141 11

  2. YADA YADA Public

    Open-source Data Ops

    Java 81 21

  3. peax peax Public

    Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

    Jupyter Notebook 67 14

  4. cellxgene-gateway 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.

    Python 52 32

  5. scar scar Public

    scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

    Python 44 4

  6. shinyValidator shinyValidator Public

    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 t…

    HTML 39 3

Repositories

Showing 10 of 86 repositories
  • 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 3 1 0 1 Updated Jun 11, 2024
  • Causal-inference-in-RCTs Public

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

    R 18 MIT 0 0 0 Updated Jun 7, 2024
  • bamdd Public

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

    TeX 14 GPL-2.0 2 0 0 Updated Jun 5, 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

    Python 44 4 0 0 Updated May 28, 2024
  • pisces Public

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

    Python 28 Apache-2.0 3 11 0 Updated May 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 0 GPL-3.0 0 0 0 Updated May 17, 2024
  • WATCH Public

    An R-repository to implement a double robust version of the WATCH workflow published in Sechidis et al. (2024)

    R 0 MIT 0 0 0 Updated May 17, 2024
  • torchsurv Public

    Deep survival analysis made easy

    Python 37 MIT 5 4 1 Updated Apr 29, 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 27 GPL-3.0 0 0 0 Updated Apr 29, 2024
  • TF_Prioritization_Benchmark_GB2023 Public

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

    0 MIT 0 0 0 Updated Apr 17, 2024
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