kkdey

Kushal K Dey's repositories

GSSG

Gene Set + S2G strategy annotations analyzed for disease architecture

Language:R43 3 31

CountClust

A R package for Grade of Membership model and Visualization of counts data:

Language:R32 7 29

Logolas

R package for Enrichment Depletion Logos (EDLogos) and String Logos

Language:RGPL-3.027 4 23

CorShrink

R package for adaptive correlation and covariance matrix shrinkage.

Language:RGPL-3.023 3 2

aRchaic

Exploration, clustering, visualization and classification of DNA damage patterns

Language:RGPL-3.018 6 7

classtpx

An R package for Semi-supervised Topic models

Language:R600

ecostructure

Clustering and Visualization of species abundance patterns in ecological data

Language:RGPL-3.06 6 8

Imperio

Repository for performing DeepBoost, S2G linking and Imperio models linking deep learning models with complex traits

Language:R6 20

CREGENE_GWAS_benchmark

Benchmarking different ENCODE CRE-gene links based on disease heritability

Language:R100

dashr

R package for Dirichlet adaptive shrinkage and smoothing

Language:R1 20

GxT

GxT is a software interface for computing gene trait association score

MIT100

maptpx

map estimation of topic models

Language:R100

methClust

Grade of Membership clustering in methylation data

Language:C100

Robocov

Sparse and Robust estimation of covariance, correlation and precision matrices when data has missing entries

Language:R100

singlecellLDSC

single cell + disease

Language:HTML100

wallace_analysis

Bird presence absence data analysis around Wallacea

Language:RNOASSERTION1 20

fineboostR

R package for performing kernel-based FS-boost fine-mapping method with applications to genetic data

Language:R000

Black_magazines

Word2vec + Statistical analysis of Black Magazines during civil rights era

Language:RNOASSERTION000

Contrastive

Exploration with contrastive algorithms

Language:Jupyter Notebook010

CorShrink-pages

A webpage for the CorShrink R package

Language:RNOASSERTION020

CorShrink2

Workflow for follow up work on CorShrink

Language:R000

cV2F

A consensus variant-to-function scoring algorithm (ENCODE, IGVF)

Language:R000

dashr-pages

A repository containing the analysis related to Dirichlet Adaptive Shrinkage (dash)

Language:RNOASSERTION020

kkdey.github.io

Personal webpage

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Logo-review

A Brief History of Logo plots

Language:R020

Logolas-pages

Workflow and webpage for the Logolas R package

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methClust-pages

Repository for testing the methClust R package

Language:RNOASSERTION000

NMF0

A fast scalable method for performing Non-negative Matrix Factorization for Biological data

Language:R000

Robocov-pages

A repository for the analysis in the Robocov paper. Dey and Mazumder 2020 bioRxiv

Language:TeX020

sequenceCNNannot

genomic sequence -> CNN -> annotation

Language:Python010