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scbatchpaper

Code used for the single-cell RNA-Seq batch effects paper

scdeepsort

Reference-free Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

scdney

Single cell data integrative analysis

scenicprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

scfba

scgen

Single cell perturbation prediction

sci-fate_analysis

Downstream analysis script for sci-fate (TF-gene linkage analysis / cell linkage analysis)

sci-hub-liberator

interface to Sci-Hub (to avoid firewall blocking)

scikit-learn-mooc

scikit-learn-mooc

scmap-paper-figures

Scripts to recreate figures from the scmap paper

scnn

Survival Convolutional Neural Networks

scrna-seq-pipelines

Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"

scrna2019

supporting code for the multinomial single cell RNA-Seq paper

scrnagan

Training Generative Adversarial Network models for scRNA-seq datasets

scrnaseq-analysis-notes

my scRNAseq analysis notes

scrnaseq-wgan-gp

Wasserstein Generative Adversarial Network for analysing scRNAseq data

scrnaseq_benchmark

Bench-marking classification tools for scRNA-seq data

sctcwhatateam

sctyper

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

segregated-dendrite-deep-learning

Deep learning in a spiking neural network using segregated dendrites.

self-assembling-manifold

The Self-Assembling-Manifold (SAM) algorithm.

seximm

sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

shinygam

sibilant

single-cell-analysis-flow-cytometry

To reveal the cellular heterogeneity within flow cytometry data, clustering and pseudotime analysis can be performed. Here, we demonstrate how to import (clustered) data, how to apply clustering and dimensionality reduction, and how to apply pseudotime analysis by Slingshot.

single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

singlecell_pnm

:sparkles: Code and figures accompanying the paper, "Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neuron differentiation" by Song and Botvinnik, et al

singlesplice

Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: http://nar.oxfordjournals.org/content/early/2016/01/05/nar.gkv1525.full

snatac

Ren Lab in-house dual-barcode single nucleus ATAC-seq (snATAC-seq) analysis pipeline