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scanpy

Single-cell analysis in Python. Scales to >1M cells.

scde

R package for analyzing single-cell RNA-seq data

scgcl

scGCL: an imputation method for scRNA-seq data based on Graph Contrastive Learning

scib

Benchmarking analysis of data integration tools

scib-pipeline

Snakemake pipeline that works with the scIB package to benchmark data integration methods.

scib-reproducibility

Additional code and analysis from the single-cell integration benchmarking project

scnova

scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis

scripts

scrna-seq

scrnaseq-analysis-notes

scRNAseq analysis notes from Ming Tang

scvelo

RNA Velocity generalized through dynamical modeling

second_challenge_evaluation

Repository for codes, analyses and visualizations for the CAMI II challenges

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

seurat

R toolkit for single cell genomics

shapeit4

Segmented HAPlotype Estimation and Imputation Tool

shasta

Experimental software for de novo assembly from Nanopore sequencing data.

single-cell-atlas-of-the-human-brain-vasculature-accross-development-adulthood-and-disease

Molecular atlas of the human brain vasculature accross development, adulthood and disease at the single-cell level

slidecna

slide_seqv2

notebooks for loading Slide-seqV2 data and some associated analyses

spatial-lung-fibrosis

Repository for all R scripts used for the bioinformatic analyses of the mouse and human 10x Genomics Visium spatially resolved transcriptomics data presented in our associated manuscript.

spatialglue

SpatialGlue is a novel deep learning methods for spatial multi-omics data integration.

swan_vis

A Python library to visualize and analyze long-read transcriptomes

trackviewer

A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot

tutorial-template

Template for the Read the Docs tutorial

ukb_rap

Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.

veritymap

workshop-scrnaseq

Single cell RNA sequencing analysis course