randel

MIND

Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution

MixRF

A random-forest-based approach for imputing clustered incomplete data

COVID-19-US-county-map

EnsDeconv

Ensemble Deconvolution to robustly estimate cellular fractions from bulk omics data

mvMISE

A General Framework for Multivariate Mixed-Effects Selection Models with Potential Missing Data

ofGEM

A Meta-Analysis Approach with Filtering for Identifying Gene-Level Gene-Environment Interactions

HiDecon

Hierarchical cellular deconvolution

bMIND_GTEx8_signif_region_CTS_eQTLs_cis

caret

caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models

cellmix

Read-only mirror of "cellmix" from r-forge SVN.

clusterProfiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

scMD

Cell type deconvolution of bulk DNA methylation data using single-cell DNA methylation references

code

coloc2

Upgrade to coloc

csSAM

Cell type-Specific Statistical Analysis of Microarray

DWLS

Gene expression deconvolution using dampened weighted least squares

EnsDeconv_shiny

Shiny app for Cell Type Deconvolution

EpiDISH

This package contains a reference-based function to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.

iRafNet

:exclamation: This is a read-only mirror of the CRAN R package repository. iRafNet — Integrative Random Forest for Gene Regulatory Network Inference. Homepage: https://www.r-project.org

LinSeed

Linseed: LINear Subspace identification for gene Expresion Deconvolution

lme4

Mixed-effects models in R using S4 classes and methods with RcppEigen

methylCC

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms

MODE

mvMISE_simulation

Simulation code and functions for mvMISE (https://github.com/randel/mvMISE)

PsychENCODE-DSPN

#DSPN

randel.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

RNA-seq

A shell pipeline for automatically analyzing all RNA-seq data in a folder based on STAR-RSEM and GATK

rseqR

An R-based pipeline to analyse RNA-seq data. This pipeline performs quality control of reads, generates gene and transcript level counts, performs differential analysis, and gene pathway enrichment analyses.

seurat

R toolkit for single cell genomics

SOUPR

SOUP, for Semi-sOft clUstering with Pure cells.