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sc_batch_remove

Wrapper of batch removal method for scRNA-seq

scrnaseq_batcheffects

Batch effects in scRNA-seq and their impact on downstream analysis

scrnaseqpipeline

scvi

A deep generative model for gene expression profiles from single-cell RNA sequencing

seurat

R toolkit for single cell genomics

seuratwgcna

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

shinycircos

an R/shiny application for creation of Circos plot interactively

single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods

single-cell-bioinformatics-scrm-2016

Single cell bioinformatics class at the Sanford Consortium for Regenerative Medicine (SCRM) in 2016

singlecellworkflow

Tutorial for the analysis of scRNA-seq data in R

somerecords

Some very useful records for me.

spectrum-of-differentiation-supplements

Mirror of analysis files for "Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells"

sra2r

SRA2R, a package to import SRA data directly into R

sradbv2

R Interface to the NCBI SRA metadata

stream

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

tdamapper

(R package) Analyze High-Dimensional Data Using Discrete Morse Theory

thymusatlastools

R package to accompany our recent Immunity paper on the mouse thymus developmental cell atlas.

tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data

umap

Uniform Manifold Approximation and Projection

urd

URD - Reconstruction of Branching Developmental Trajectories

utilities

Useful perl code for NGS analysis. Primarily GFF3 manipulation and FASTA parsing.

velocyto-notebooks

velocyto.py

RNA velocity estimation in Python

velocyto.r

RNA velocity estimation in R

vision

A high-throughput and unbiased module for interpreting scRNA-seq data.

workshop-scrnaseq-oxford-sep2016

scRNA-seq workshop in Oxford on 9 September 2016