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scde

R package for analyzing single-cell RNA-seq data

scfba

scfea

single cell Flux Estimation Analysis (scFEA)

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

sclvm

scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.

scorpius

Trajectory inference for single-cell RNA-seq

scrna.seq.course

Analysis of single cell RNA-seq data course, Cambridge University, UK

scrnaseqpipeline

scw

HSCI/Catalyst Single-cell RNA-Seq Workshop

seastar

SEASTAR - Systematic Evaluation of Alternative transcription STArt site in RNA

seqcomplex

Algorithms to compute DNA complexity

seurat

R toolkit for single cell genomics

shinycircos

an R/shiny application for creation of Circos plot interactively

single-cell-pseudotime

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

single-cell-rna-seq

A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.

single_cell_portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

single_cell_portal_core

Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

singler

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)

singlesail

A toolkit to help sail you through single-cell analyses

slidifyexamples

Sample Presentations

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

snakepipes

A toolkit based on snakemake and python for analysis of NGS data

souporcell

Clustering scRNAseq by genotypes

spacedeconv

A unified interface to spatial transcriptomics deconvolution tools

spade

SPADE: Spanning Tree Progression of Density Normalized Events

spateo-release

Spatiotemporal modeling of spatial transcriptomics

spatial_scog_workshop_2022

Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022

spatialanalysisworkflows

spatialtranscriptomics

Pipeline for processing spatially-resolved gene counts with spatial coordinates, image data, and optionally single cell RNA-seq data, designed for 10x genomics visium and single cell transcriptomics.

splicelauncher

RNAseq pipeline for alternative splicing junctions