Gifford Lab, MIT CSAIL

prescient

Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.

antibody-2019

optivax

overinterpretation

Code for Overinterpretation paper

DeepLigand

PUFFIN

ReprogrammingRecovery

Code for creating consensus motif database and performing motif enrichment

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.

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).

FactorizableLibrary

Code and data for factorizable libraries

skipguide

Predictive model for CRISPR-Cas9 mediated Exon Skipping

idr2d

Irreproducible discovery rate for genomic interaction data

seqgra

seqgra: Synthetic rule-based biological sequence data generation for architecture evaluation and search

6884-antibodies-data

Problem Set 2 Data

DeepAccess

Code for training, testing, and motif extraction from multilabel DNA sequence ensemble of convolutional neural networks

DiminishingReturns

Constrained Submodular Optimization

gifford-lab.github.io

New group website.

MHC2-optimization

MIT-T-COVID-vaccine

Code for MIT-T-COVID vaccine paper

spatzie

Identification of enriched motif pairs from chromatin interaction data

counterselection

counterselection

disentangled

High-Resolution-STARRseq

Starrseq Analysis with the Sherwood Lab

MIAA-analysis

mit-6.881

mit-6.S977

mit-6884.github.io

Computational Aspects of Therapeutic Design

motor-neuron-maturation

Supporting code for motor neuron maturation manuscript

PIQ

skipguide-analysis