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baynorm

Normalization for single cell RNA-seq data

bioinfo2019

cistopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

clint_coronary_snatac_naturegenetics

cna_combined_with_ml

Code to compute network properties (features) for subgraphs of a correlation-based network

coefexplainer

Understand How to Interpret the Coefficients of a Categorical Linear Model

conquer_comparison

Code for evaluation of differential expression methods in single-cell RNA-seq data

cytoscape_workflows

collection of notebooks with different cytoscape workflows

deepimpute

An accurate and efficient deep learning method for single-cell RNA-seq data imputation

dev-kidney-snatac

Codes used in the developmental kidney snATAC-seq data

dge_workshop

dynbenchmark

Comparison of methods for trajectory inference on single-cell data 🥇

figr

Functional Inference of Gene Regulation

ft-lab

gchromvar

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

gimap_tools

Tools for processing and analyzing pooled Genetic Interaction map data

hotspot_analysis

Analysis scripts for writing the Hotspot paper

humanbreast10x

Code for scRNA seq analysis Integration

image-based-cell-profiling-enhancement-via-data-cleaning-methods

integration2019

intro-to-python-cwml-workshop

kerala_gov_hdi_comparison

Comparing HDI increase in kerala gov.

ldsc-corrplot-rg

corrplot of LDSC genetic correlation results

lymph_node_project

List of all R codes used for the analysis of single cell data in the paper Blecher et al. on the study of immune cell communications.

meld

Quantifying experimental perturbations at single cell resolution

metaneighbor

A method to rapidly assess cell type identity using both functional and random gene sets

mimosca

A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.

mit-o-matic

Automatically exported from code.google.com/p/mit-o-matic

mrlocus

Mendelian Randomization of gene expression (exposure) on GWAS traits (outcome). See website for software usage guide:

ncomms-20-00614