bernardo-de-almeida

basepairmodels

deeplift

Public facing deeplift repo

DeepSTARR

Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Drosophila melanogaster S2 cells

DeepSTARR_embryo

Deep learning models to predict enhancers in different Drosophila embryo tissues

Enformer_predictions

Code to use the Enformer model to make predictions on new sequences

models

Model zoo for genomics

motif-clustering

Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy

Neural_Network_DNA_Demo

Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction

PanCancer_CentrosomeAmplification

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome

Variant_STARRseq

Scripts to reproduce the results of the random variant and oligo STARR-seq paper

bernardo-de-almeida/DeepSTARR

Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Drosophila melanogaster S2 cells

bernardo-de-almeida/motif-clustering

Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy

bernardo-de-almeida/DeepSTARR_embryo

Deep learning models to predict enhancers in different Drosophila embryo tissues

bernardo-de-almeida/PanCancer_CentrosomeAmplification

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome

bernardo-de-almeida/Enformer_predictions

Code to use the Enformer model to make predictions on new sequences

bernardo-de-almeida/Neural_Network_DNA_Demo

Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction

bernardo-de-almeida/Variant_STARRseq

Scripts to reproduce the results of the random variant and oligo STARR-seq paper

bernardo-de-almeida/basepairmodels

bernardo-de-almeida/deeplift

Public facing deeplift repo

bernardo-de-almeida/models

Model zoo for genomics

bernardo-de-almeida/Neural_machine_translation

Sequence-to-sequence Transformer model to translate Portuguese into English

bernardo-de-almeida/Sentiment_classification_BERT

Language model for sentiment analysis

bernardo-de-almeida/tfmodisco

TF MOtif Discovery from Importance SCOres