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covid-sequence-analysis-workflow

covid19-gene-sequence-analysis

Analyzing the sequence of COVID-19 and comparing it to sequences of viruses that are known to cause pandemics using the Knuth-Morris-Pratt Algorithm.

covid19-protein-sequence-analysis

d-gex

Deep learning for gene expression inference

dca

Deep count autoencoder for denoising scRNA-seq data

dcc

This repository contains the source code and data for reproducing results of Deep Continuous Clustering paper

dcec

de-analysis

dec

deep-representations-clustering

This repository is an attempt to replicate the results for the paper: "Learning Deep Representations for Graph Clustering".

deep-subspace-clustering-networks

deepembeddedclustering

Tensorflow implementation of Deep Embedded Clustering (DEC) for unsupervised learning

dgca

Differential Gene Correlation Analysis

doubletdecon

A tool for removing doublets from single-cell RNA-seq data

doubletfinder

R package for detecting doublets in single-cell RNA sequencing data

dropletqc

Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data

epat

equine_lncrna

equine lncRNA discovery pipeline

fastrna

FastRNA: Single-cell analysis of atlas-scale data on a laptop

fly-atac

Code relevant to sci-ATAC-seq of Drosophila embryogenesis.

gaussian_mixture_vae

gbmap

Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

gemsec

The TensorFlow reference implementation of 'GEMSEC: Graph Embedding with Self Clustering' (ASONAM 2019).

ggsignif

Easily add significance brackets to your ggplots

giniclust

GiniClust: Detecting Rare Cell Types from Single-Cell Gene Expression Data with Gini Index

gmvae

Deep Unsupervised Clustering with Gaussian Mixture Variational Autoencoders

gsrc

various sources and scripts for genomic research software

gutils

Utility functions to extend and optimize GenomicRanges functionality.

idec

idec-pytorch

Pytorch implementation of Improved Deep Embedded Clustering