andreamrau Goto Github PK

2022_digit-bio_workshop

2022 DIGIT BIO workshop materials: "Do my clusters make sense? Some statistical and biological clues to help..."

andrea

andreamrau.github.io

bayesr

Bayesian hierarchical model for complex trait analysis

bayesr_simulations

blogdown_source

Repo to store blogdown site source content

clustree

Visualise Clusterings at Different Resolutions

coolkit

coseq

Co-Expression Analysis of Sequencing Data

cv

ebdbnet

Infer the adjacency matrix of a network from time course data using an empirical Bayes estimation procedure based on Dynamic Bayesian Networks.

edge-in-tcga

Source code to reproduce results from "Exploring Drivers of Gene Expression in The Cancer Genome Atlas" by Rau et al. (2017)

firebrowser

An R client for broads firehose pipeline, providing TCGA data sets

gbncausal

Causal estimation for Gaussian Bayesian networks

htscluster

Clustering High-Throughput Transcriptome Sequencing (HTS) Data with Poisson Mixture Models

htsfilter

Filter replicated high-throughput transcriptome sequencing data

maskmeans

Multi-view agglomeration/splitting K-means clustering algorithm

miscr

Some miscellaneous R code

opticregen_2019

Source code for RNA-seq and ATAC-seq results presented in Dhara et al. (2019)

padma

Pathway deviation scores using multiple factor analysis

rifplus

rmfrjla_2019

Code for producing the analysis in the "Individualized multi-omic pathway deviation scores using multiple factor analysis" manuscript

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rosetta

Regeneration Rosetta: An interactive R/Shiny app to explore regeneration-associated gene expression and chromatin accessibility

rpkg-min

rpl

Randomized pairwise likelihood method for complex statistical inferences

shinygeo

shinyGEO Homepage -http://gdancik.github.io/shinyGEO/

tidyqtldb

Format AnimalQTLdb annotations for use with BayesRCO

tp-rgcca

Présentations et codes reproductibles présentés lors de la journée StatOmique du 13 juin