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10xcellranger

RNAseq pipeline for 10X protocol

bioconductor-sc3-scripts

Wrapper scripts for the SC3 R package

bustools_mapping_workflow

Repository for the mapping of single cell data using `bustools`

cartal.github.io

Build a Jekyll blog in minutes, without touching the command line.

cellstates

Finding gene expression states in scRNA-seq data

dp_gp_cluster

galaxy-sc3-wrappers

Galaxy wrappers scripts for SC3

hca_heart

This is the official repository for the Human Cell Atlas Heart project.

ifnarko_microglia_ecm

Files from the analysis of WT and KO transcriptomes from purified microglia in C57Bl6 mice

lisbon_single_cell_2021

Repository for the notebooks used in the Single Cell workshop for the Lisbon Summer School 2021

mda_hepatocytes

multiomic_benchmark

Comparison of multi-omic integration methods for single-cell data.

sc-tertiary-file-format-specs

A place to store and version specifications for file formats associated with downstream single-cell analysis

scatac_prep

A not-too-orderly collection of scripts for preprocessing and dimensionality reduction of scATAC-seq data

scbrie2

Repository for scRNA-Seq splice variant detection mapping using STARsolo and BRIE2

scgen

scjp

this is package to assist python based single-cell analysis

scvi

Deep generative modeling for single-cell transcriptomics

scvi-tutorials

Notebooks used in scvi-tools tutorials

spleen_vs_blood_microarray

Analysis of microarray expression data for Malaria

statistical-rethinking

Solutions for the practice problems

symphony

Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seq

talaveralopezlab.github.io

tci_analyses

Scripts used for the Trypanosoma cruzi TcI population genomics study

trvae

Conditional Out-of-Sample prediction

velocyto.py

RNA velocity estimation in Python

viral-mutation

A from frmom Brian Hie's Language modeling of viral evolution