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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

code

coloc2

Upgrade to coloc

covid-19-us-county-map

cssam

Cell type-Specific Statistical Analysis of Microarray

dwls

Gene expression deconvolution using dampened weighted least squares

ensdeconv

Ensemble Deconvolution to robustly estimate cellular fractions from bulk omics data

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.

hidecon

Hierarchical cellular deconvolution

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

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

mvmise

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

mvmise_simulation

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

ofgem

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

pcamethods

R package for performing PCA with applications to missing value imputation

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.

scmd

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

seurat

R toolkit for single cell genomics

soupr

SOUP, for Semi-sOft clUstering with Pure cells.