The Bhardwaj Lab is a part of the Institute of Biodynamics and Biocomplexity of Utrecht University. We study regulatory genomics of cell fate decisions. We build new bioinformatic methods and tools to analyse data from emerging genomics technologies.
Bhardwaj Lab
Quantitative Biology and Data Integration group, Utrecht University
- 5 followers
- Netherlands
- https://vblab.org
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scChICflow
scChICflow PublicWorkflow for processing single-cell ChIC (Chromatin ImmunoCleavage) data
Python 2
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ecosystem-packages
ecosystem-packages PublicForked from scverse/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
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A command-line and python toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data
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Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression).
- PPO-agent-framework-Cellular-reprogramming Public Forked from CBannink/PPO-agent-framework-Cellular-reprogramming
Designed and trained an ppo agent to predict which sequences of alterations are necessary to shift a cell's identity from a start state into any desired target (for which it is trained at least)
- ecosystem-packages Public Forked from scverse/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
- Optimized-CellOracle Public Forked from CBannink/Optimized-CellOracle
Modified CellOracle package used as the environment simulator for RL-guided cellular reprogramming. Integrated GPU access through Cupy or optimized matrix multiplications through smart idexing with Numpy instead of Pandas. Able to perform targeted alterations on single cells.
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