francescopatane96

scKD

escape

Easy single cell analysis platform for enrichment

speckle

R package for specialised analysis of single cell data

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

SCnorm

Normalization for single cell RNA-seq data

Notes

Personal notes about work- and coding-related topics

scone

dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

CVMC

Monte Carlo simulation of virus spread

seurat-wrappers

Community-provided extensions to Seurat

Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

SCPA

R package for pathway analysis in scRNA-seq data

SingleR

Clone of the Bioconductor repository for the SingleR package.

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

scProportionTest

UCell

Gene set scoring for single-cell data

single-cell-best-practices

https://www.sc-best-practices.org

OSCA.multisample

The multi-sample subbook of OSCA

seurat

R toolkit for single cell genomics

SingleR

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

gpu-burn

Multi-GPU CUDA stress test

celltypist_wiki

Materials and scripts for building cell type encyclopedia table

celltypist

A tool for semi-automatic cell type classification

Contributions

Contribute Packages to Bioconductor

sc-type

sphere

DIYbiosphere is an open-source project to collect Do-it-Yourself Biology (DIYbio) initiatives from all over the world

Minesweeper

Genome Design Algorithm for Minimal Genomes using Whole Cell Models

WholeCellEcoliRelease

Release of the whole cell E. coli model.