Pinned Repositories
antibody-2019
CpGenie
deepbind-docker
Docker image for the DeepBind method.
DeepLigand
jupyter-docker-stacks
Opinionated stacks of ready-to-run Jupyter applications in Docker. Forked to add GPU capabilities.
Keras-genomics
Perform hyper-parameter tuning, training, testing and prediction with Keras
optivax
overinterpretation
Code for Overinterpretation paper
prescient
Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
PUFFIN
Gifford Lab, MIT CSAIL's Repositories
gifford-lab/prescient
Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
gifford-lab/antibody-2019
gifford-lab/optivax
gifford-lab/overinterpretation
Code for Overinterpretation paper
gifford-lab/DeepLigand
gifford-lab/PUFFIN
gifford-lab/ReprogrammingRecovery
Code for creating consensus motif database and performing motif enrichment
gifford-lab/deepaccess-package
Methods for training and interpretation of an ensemble of neural networks for multi-task functional prediction of accessibility or histone modifications from DNA sequence.
gifford-lab/prescient-analysis
Notebooks for pre-processing, analysis, and visualization of PRESCIENT applied to in vitro hematopoeisis (Weinreb et al. 2020) and in vitro beta-cell differentiation (Veres et al. 2019).
gifford-lab/FactorizableLibrary
Code and data for factorizable libraries
gifford-lab/skipguide
Predictive model for CRISPR-Cas9 mediated Exon Skipping
gifford-lab/idr2d
Irreproducible discovery rate for genomic interaction data
gifford-lab/seqgra
seqgra: Synthetic rule-based biological sequence data generation for architecture evaluation and search
gifford-lab/6884-antibodies-data
Problem Set 2 Data
gifford-lab/DeepAccess
Code for training, testing, and motif extraction from multilabel DNA sequence ensemble of convolutional neural networks
gifford-lab/DiminishingReturns
Constrained Submodular Optimization
gifford-lab/gifford-lab.github.io
New group website.
gifford-lab/MHC2-optimization
gifford-lab/MIT-T-COVID-vaccine
Code for MIT-T-COVID vaccine paper
gifford-lab/spatzie
Identification of enriched motif pairs from chromatin interaction data
gifford-lab/counterselection
counterselection
gifford-lab/disentangled
gifford-lab/High-Resolution-STARRseq
Starrseq Analysis with the Sherwood Lab
gifford-lab/MIAA-analysis
gifford-lab/mit-6.881
gifford-lab/mit-6.S977
gifford-lab/mit-6884.github.io
Computational Aspects of Therapeutic Design
gifford-lab/motor-neuron-maturation
Supporting code for motor neuron maturation manuscript
gifford-lab/PIQ
gifford-lab/skipguide-analysis