madhulika-ebi Goto Github PK

2019_murine_cell_aging

Tools associated with the Calico Murine Aging Cell Atlas, Kimmel 2019 et. al., Genome Research

allenricher

A comprehensive gene set function enrichment tool for multiple species.

analysisframeworksimilartissues

The analysis framework of gene expression data in case the sample groups are very similar.

batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

beval

biodiscml

Large-scale automatic feature selection for biomarker discovery in high-dimensional OMICs data

combat-seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

decode

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

iterativewgcna

Extension of the WGCNA program to improve the eigengene similarity of modules and increase the overall number of genes in modules.

meta-analysis

Selection of genes to be cultured and studied on-board for the AcubeSAT nanosatellite project. Microarray data analysis in R. Meta-analysis in R. Literature review and more

ml-pipeline

Shiu Lab code base for Machine Learning implemented in SciKit-Learn

pipeline-for-batch-effect-correction-in-baseline-experiments

Pipeline for batch effect correction in Baseline experiments proposed by Guillaume HEGER, trainee in Gene Expression Team, EMBL-EBI in 2019

renv-docker

A guide to getting {renv} projects into Docker images

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rnaseq-workflow

A repository for setting up a RNAseq workflow

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.

run-wgcna

Wrapper R scripts for performing a weighted-gene co-expression network analysis (WGCNA)

scientific-visualization-book

An open access book on scientific visualization using python and matplotlib

scrattch.hicat

Hierarchical, iterative clustering for analysis of transcriptomics data in R

scwgcna

Weighted gene co-expression network analysis for scRNA-seq data in Seurat

single-cell-metabolic-landscape

Pipeline for exploring metebolic heterogeneity at single-cell resolution

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

testing

to-gcn

Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) data

wgcna-vae