PedroMilanezAlmeida

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Rcpp

Seamless R and C++ Integration

fgsea

Fast Gene Set Enrichment Analysis

PCAtools

PCAtools: everything Principal Components Analysis

miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

uwot

An R package implementing the UMAP dimensionality reduction method.

scattermore

very fast scatterplots for R

sctransform

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

ggdark

Dark mode for ggplot2 themes

glmGamPoi

Fit Gamma-Poisson Generalized Linear Models Reliably

glmpca

CelliD

Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.

lemur

Latent Embedding Multivariate Regression

Sanity

Filtering of Poison noise on a single-cell RNA-seq UMI count matrix

dsb

Normalize CITEseq Data

SCPA

R package for pathway analysis in scRNA-seq data

miloDE

Framework for sensitive DE testing (using neighbourhoods)

contrastive-ne

Contrastive neighbor embeddings

scar

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

umi-normalization

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

rcpphnsw

Rcpp bindings for the approximate nearest neighbors library hnswlib

transformGamPoi-Paper

EmbedSOM

Fast embedding ot multidimensional datasets, great for cytometry data

mrvi_archive

Multi-resolution Variational Inference

scPrisma

scPrisma is a spectral analysis method, for pseudotime reconstruction, informative genes inference, filtering, and enhancement of underlying cyclic signals

clusterpval

rnndescent

R package implementing the Nearest Neighbor Descent method for approximate nearest neighbors

clusterpval-experiments

10x-cd45-isoform-quantification

faust_simulation_study