kvshams

HumanBreast10X

Code for scRNA seq analysis Integration

bayNorm

Normalization for single cell RNA-seq data

cisTopic

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

Clint_Coronary_snATAC_natureGenetics

CoefExplainer

Understand How to Interpret the Coefficients of a Categorical Linear Model

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

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

Hotspot_Analysis

Analysis scripts for writing the Hotspot paper

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

intro-to-python-cwml-workshop

kerala_gov_hdi_comparison

Comparing HDI increase in kerala gov.

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.

mrlocus

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

NCOMMS-20-00614

One2One

This package is used to get 1:1 orthologs based on MGI homology data from http://www.informatics.jax.org/homology.shtml

open_chromatin

Repo for https://www.biorxiv.org/content/10.1101/427484v2

RaceID3_StemID2_package

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and StemID2 method including novel functionalities and performance improvements compared to the previous RaceID3/StemID2 version in the RaceID3_StemID2 repository. The RaceID3_StemID2 repository will not be updated anymore in the future.

scMatch

scMatch: a single-cell gene expression profile annotation tool using reference datasets

scRNA-seq_topic_modeling

Single Cell RNA-seq Analysis by Topic Modeling

seurat-disk

Interfaces for HDF5-based Single Cell File Formats

SingleCellJugaad

These are the scripts used for common data manipulations in various single cell tools and analysis

SingleCells_SLE_paper

Scripts used for the analysis of single cell SLE PBMCs

SingleCellSignalR_v1

R package