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bedoverlapsdb

brapes

BCR reconstruction from short single cell RNA-seq

cassiopeia

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

census-scvi

compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes

compassr

An R library for conducting analyses on COMPASS data.

condition_connectivity_problems

Algorithms for connectivity problems in condition-varying protein networks

criticism-tutorials

Notebooks used in scvi-criticism tutorials

czi-immuneaging

destvi_utils

Utilities for downstream analysis of destVI

dynamic_connectivity

Algorithms for connectivity problems in time-varying protein networks

embedding-scvi

epitome

Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility

fastproject

Dimensionality reduction for single cell RNA-seq data

hotspot

immunity2022

Analysis repo for Pawlak and DeTomaso et. al, Immunity 2022

impulsede

ImpulseDE

impulsede2

keris

A framework for identifying systematic variation at the single-cell level by leveraging low-resolution population-level data

lineagepulse

Differential expression analysis for single-cell RNA-seq data

mpra_featurization

Featurizer for MPRA and other analyses. Can run DeepSea, Deepbind, epigenetic features, 5mer counts, Encode motif matrix, DNA shape, conservation, and some sequence features

mpranalyze

Analyse enhancer strength based on MPRA experiments.

mrvi

Multi-resolution Variational Inference

mrvi-reproducibility

Nextflow pipeline for MrVI pipelines

mrvi_archive

Multi-resolution Variational Inference

phyloplot

A library of Plotly functionality for plotting phylogenies.

popv

popv-reproducibility

Reproducibility for popV

pycea

scverse lineage tracing analysis toolkit

rline

R wrapper around the LINE algorithm for network embedding