adamklie

adamklie's Stars

• MisaOgura/flashtorch

  Visualization toolkit for neural networks in PyTorch! Demo -->

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• cggh/scikit-allel

  A Python package for exploring and analysing genetic variation data

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• CompEpigen/figeno

  Tool for plotting sequencing data along genomic coordinates.

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• scikit-learn-contrib/skglm

  Fast and modular sklearn replacement for generalized linear models

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• aertslab/AUCell

  AUCell: score single cells with gene regulatory networks

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• vanheeringen-lab/gimmemotifs

  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

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• calico/borzoi

  RNA-seq prediction with deep convolutional neural networks.

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• manzt/pygv

  a minimal, scriptable genome browser for python

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• snehamitra/SCARlink

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• pinellolab/pychromVAR

  A python package for chromVAR

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• rs239/velorama

  Gene regulatory network inference for RNA velocity and pseudotime data

  Language:Python22264

• sjgosai/boda2

  Computational Optimization of DNA Activity (CODA)

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• GfellerLab/MetacellAnalysisToolkit

  Toolkit for metacell analysis

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• kundajelab/ProCapNet

  Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.

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• ekernf01/perturbation_benchmarking

  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.

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• kundajelab/DART-Eval

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• IliasGeoSo/TFBSs_grammar

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• jvtalwar/GRIEVOUS

  GRIEVOUS: Generalized Realignment of Innocuous and Essential Variants Otherwise Utilized as Skewed

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• Wenhao-Jin/HydRA

  A deep-learning model for predicting RNA-binding capacity from protein interaction association context and protein sequence

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• aertslab/DeepBrain

  DeepBrain: a collection of vertebrate sequence-based enhancer models aimed at understanding brain cell type enhancer code across and within species

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• aertslab/scatac_fragment_tools

  Tools for working with scATAC-seq fragment files

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• suinleelab/deepprofile-study

  Code for paper "A deep profile of gene expression across 18 human cancers"

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• EngreitzLab/sc-E2G

  Pipeline to run sc-E2G

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• johli/aparent-perturb

  A multi-task neural network for predicting perturbation responses to Alternative Polyadenylation usage levels

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• mostafavilabuw/MPRACollection

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• ekernf01/ggrn

  Python implementation for a flexible Grammar of Gene Regulatory Network inference methods (GGRN)

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• ekernf01/network_collection

  A collection of gene regulatory networks, mostly but not entirely from chromatin data & ChIP or motif analysis.

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• ekernf01/pereggrn

  Infrastructure for benchmarking tools that predict perturbation responses.

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• ekernf01/perturbation_data

  A collection of transcriptomic data on genetic perturbations.

  Language:Jupyter Notebook1200

• Gaulton-Lab/non-diabetic-islet-multiomics

  Code and references used to process 10x Multiome data from pancreatic islets and perform analyses of phenotype and genotype associations with islet physiology

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