ninashenker

EagleC

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps

HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

rnafusion

RNA-seq analysis pipeline for detection of gene-fusions

NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

bioconda-recipes

Conda recipes for the bioconda channel.

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

mae

PyTorch implementation of MAE https//arxiv.org/abs/2111.06377

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

Methylation

DNA methylation for tumor subclassifications by methylation array.

nextflow

A DSL for data-driven computational pipelines

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

MACS

MACS -- Model-based Analysis of ChIP-Seq

maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

C.Origami

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Histomorphological-Phenotype-Learning

Corresponding code of 'Quiros A.C.+, Coudray N.+, Yeaton A., Yang X., Chiriboga L., Karimkhan A., Narula N., Pass H., Moreira A.L., Le Quesne J.*, Tsirigos A.*, and Yuan K.* Mapping the landscape of histomorphological cancer phenotypes using self-supervised learning on unlabeled, unannotated pathology slides. 2024'

BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

sphinx

The Sphinx documentation generator

fastMRI

A large-scale dataset of both raw MRI measurements and clinical MRI images.

ENCODE_downloader

Downloader for ENCODE

TED

a fully Bayesian approach to deconvolve tumor microenvironment

hic-bench

A set of pipelines for Hi-C and ChIP-Seq analysis.

DWLS

Gene expression deconvolution using dampened weighted least squares

iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

DeepPATH

Classification of Lung cancer slide images using deep-learning

atlas

ATLAS - Three commands to start analyzing your metagenome data

tullie_files

transformers

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

deepbin

Improved metagenome binning using transformers