Al-Murphy

Al-Murphy's Stars

• google-deepmind/deepmind-research

  This repository contains implementations and illustrative code to accompany DeepMind publications

  Language:Jupyter Notebook13.3k3253252.6k

• lh3/seqtk

  Toolkit for processing sequences in FASTA/Q formats

  Language:C1.4k62176307

• duerrsimon/bioicons

  A library of free open source icons for science illustrations in biology and chemistry

  Language:Vue1.4k174978

• Pold87/academic-keyword-occurrence

  Extracts the historic word occurrence of a search term in academic papers

  Language:Python302101087

• Genentech/gReLU

  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

  Language:Python23194023

• deeptools/pyBigWig

  A python extension for quick access to bigWig and bigBed files

  Language:C218610149

• jmschrei/tangermeme

  Biological sequence analysis for the modern age.

  Language:Python194101612

• ML-Bioinfo-CEITEC/genomic_benchmarks

  Benchmarks for classification of genomic sequences

  Language:Jupyter Notebook11932017

• omerwe/polyfun

  PolyFun (POLYgenic FUNctionally-informed fine-mapping)

  Language:Python96218322

• calico/borzoi

  RNA-seq prediction with deep convolutional neural networks.

  Language:Python9552213

• jmschrei/tfmodisco-lite

  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.

  Language:Python5943817

• dohlee/chromoformer

  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

  Language:Python34382

• pinellolab/EPInformer

  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization

  Language:Jupyter Notebook33118

• EdwinTh/dutchmasters

  R package with colour palettes derived from famous paintings by 17th century Dutch masers :framed_picture:🎨 :man_artist:🇳🇱!

  Language:R31243

• kundajelab/ENCODE_downloader

  Downloader for ENCODE

  Language:Python3171211

• pfizer-opensource/bigwig-loader

  A fast dataloader for bigwig files made for machine learning

  Language:Python24501

• Genentech/decima

  Decima is a Python library to train sequence models on single-cell RNA-seq data.

  Language:Jupyter Notebook20422

• p-koo/evoaug

  Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics

  Language:Python20204

• shtoneyan/gopher

  Toolset for training quantitative sequence to function models.

  Language:Jupyter Notebook20409

• bowang-lab/genomic-FM

  Language:Python18472

• yakirr/sldp

  Signed LD profile regression code

  Language:Python174126

• mostafavilabuw/EnformerAssessment

  Language:Python14231

• neurogenomics/EnformerCelltyping

  Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) interactions to predict histone marks across diverse cell types.

  Language:Jupyter Notebook11400

• shirondru/enformer_fine_tuning

  For fine-tuning Enformer using paired WGS & gene expression data

  Language:Python113

• VariantEffect/mavehgvs

  A specification and Python implementation for representing variants from Multiplexed Assays of Variant Effect.

  Language:Python117182

• vjcitn/BiocHail

  Using hail via Basilisk

  Language:R6440

• ni-lab/finetuning-enformer

  Code for improving the performance of sequence-to-expression models for making individual-specific gene expression predictions by fine-tuning them on personal genome and transcriptome data.

  Language:Jupyter Notebook50

• H-Mateus/dri-reproducibility-template

  A standardised project template for incorporating best practices in reporducibility

  Language:Jupyter Notebook4170

• ICL-BMB-BiDS/BIDS2-DimensionReduction1

  This session is focussed on what dimension reduction is, what it can be used for and revolves around Principal Component Analysis (PCA).

  Language:Jupyter Notebook1000

• neurogenomics/chromexpress

  Which epigenetic factors are the best predictors of gene expression? An analysis using ENCODE data.

  Language:Python110