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embl-single-cell-course-2016

Material for lecture at the EMBL Single Cell Course 2016

embryotimecourse2018

Data and analysis scripts for our Embryo Timecourse paper.

enrichment_analysis_celltype

Cell type enrichment analysis using gene signatures and cluster markers

ewce

Expression Weighted Celltype Enrichment

fateid

R package for the inference of cell fate bias from single-cell RNA-seq data.

genvisr

Genome data visualizations

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics

gganimate

A Grammar of Animated Graphics

glmnet

R package glmnet for estimating lasso and elastic net

goatools

Python scripts to find enrichment of GO terms

gpfates

gseapy

Gene Set Enrichment Analysis in Python

gsva

Gene set variation analysis for microarray and RNA-seq data

gtseq-pipeline

A series of perl and python scripts for generating genotypes from NGS fastq files from GTseq library sequencing.

gwas-scrnaseq-integration

Finding enrichment in MCA cell types for published rare and common variants associated with disease traits from GWAS Catalog

hemberg-scrna-seq-course

hgnchelper

Identify and correct invalid gene symbols

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hiclink

HiClink: a scalable, flexible, robust framework for HiC data

hicplotter

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

illumina-barcode-swapping

lola

Locus Overlap Analysis: Enrichment of Genomic Ranges

magma_celltyping

Identify cell types underlying the associations found in GWAS summary statistics

merlot

Reconstruct the lineage topology of a scRNA-seq differentiation dataset.

metamap

MetaMap - This repository describes the code and analyses accompanying the "MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data" manuscript.

mouse_scrnaseq

List of mouse scRNA-Seq studies

msigdb

MSigDB gene sets

networkd3

D3 JavaScript Network Graphs from R

ngs_data_processing

Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.

noted-bugs-in-analysis-

Some Bugs need to be noted!!!!!